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revision 1827, Wed Apr 25 22:22:41 2007 UTC revision 2245, Mon Aug 25 15:06:12 2008 UTC
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1    2008-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/LU.R: expand( <sparseLU> )
4    
5            * NAMESPACE, man/all.equal-methods.Rd:
6            * R/Matrix.R (all.equal): methods for Matrices,
7            * R/sparseMatrix.R, R/sparseVector.R: sparseMatrices and -Vectors
8    
9    
10    2008-08-23  Douglas Bates <bates@stat.wisc.edu>
11    
12            * [r2243] R/CHMfactor.R, man/CHMfactor-class.Rd: Added expand method and
13              documentation for CHMfactor class
14            * [r2241] R/CHMfactor.R: Added trivial coercion method for CHMfactor ->
15              pMatrix
16    
17    2008-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/nsCMatrix.R (setAs(., dgTMatrix))): remove unused method
20    
21    2008-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/Ops.R (.Ops2dge.via.x, and many others): eliminate never-used
24            variable assignments {from "next version" codetools}.
25            * R/Csparse.R, R/Tsparse.R: ditto
26    
27    2008-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/sparseVector.R (sp2vec, coerce to sparseVector):
30            make sure no integer overflows happen, and use double precision
31            (n, index) where appropriate.
32    
33            * tests/Simple.R: test "large" sparse vectors.
34    
35    2008-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/AllClass.R (sparseVector): 'length' and 'i' are "numeric", not
38            just integer (allowing much longer length).
39    
40    2008-07-28  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/AllClass.R (diagonalMatrix): extend  "sparseMatrix" instead of
43            "denseMatrix".  This renders "scarceMatrix" dispensable and
44            invalidates part of MM's presentations on "space of Matrix
45            classes", but seems cleaner overall.
46    
47            * R/diagMatrix.R, etc: eliminate "scarceMatrix", replacing it by
48            "sparseMatrix" in method signatures;
49            further, instead of coercing to "sparseMatrix", coerce to
50            "TsparseMatrix" now.
51    
52    2008-07-26  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * src/dgCMatrix.c (dgCMatrix_qrsol): allow third argument 'order' in
55            .Call(.)
56            * R/sparseMatrix.R (lm.fit.sparse), src/dgCMatrix.h, src/init.c: ditto
57    
58    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
61            recursion in new test in
62            * tests/matprod.R: testing the above and another solve() case, below
63    
64            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
65            e.g. triangular 'x'.
66    
67            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
68            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
69            correctly with unit-triangular x
70    
71            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
72            instead of not checking diagU.
73    
74            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
75            experiments where diagonalMatrix would extend sparse*.
76    
77    
78    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
81            "x@p[ncol(x)]" instead of length(x@i).
82            * R/Auxiliaries.R (nnzero): ditto
83    
84            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
85            since that fails for over-allocated i.
86    
87            * tests/validObj.R: more testing of over-allocated (i,x) slots
88    
89    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
92            'sort_in_place' and set it to TRUE in call from
93            * src/Csparse.c (Csparse_validate): sort in place, making sure that
94            validObject() continues sort the columns if needed.
95    
96            * tests/validObj.R: now tests that more thoroughly, and
97            * man/CsparseMatrix-class.Rd: documents it.
98    
99    2008-07-22  Douglas Bates <bates@stat.wisc.edu>
100    
101            * [r2233] src/chm_common.c: sort columns more carefully in
102              as_cholmod_sparse
103            * [r2231] src/chm_common.c: check for sorted columns in
104              as_cholmod_sparse instead of assuming it
105            * [r2228] src/cs_utils.c: Use R_alloc for semi-permanent storage when
106              expanding diagonal
107    
108    
109    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
112            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
113            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
114            diagU2N().
115    
116            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
117            .spDiagonal() and new .trDiagonal().
118    
119            * R/dtCMatrix.R (solve): make use of .trDiagonal()
120    
121    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
124            stumbled upon by Michael H.
125    
126            * tests/validObj.R: testing the bug-fix
127    
128            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
129            versions.
130    
131            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
132            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
133    
134            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
135              AS_CHM_SP() which includes diagU2N.
136    
137            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
138            adapt to 3 arguments.
139    
140    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
141    
142            * [r2220] src/dtCMatrix.c: Correct number of columns for rhs in
143              dtCMatrix_sparse_solve
144            * [r2219] src/cs_utils.c: eye->nz should be -1 for compressed column
145              storage
146            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
147              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
148              new solve method
149            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
150              Csparse_diagU2N functionality into Matrix_as_cs
151    
152    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
155    
156    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
157    
158            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
159              argument with default TRUE
160            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
161              Csparse_diagU2N
162            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
163              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
164              parent array; new solve method for signature(a = "dtCMatrix", b =
165              "sparseMatrix")
166    
167    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/diagMatrix.R (.bdiag): also keep result triangular
170    
171    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
172    
173            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
174              messages
175    
176    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
179            symmetric- or nsparse-Matrix, also fixing the bug introduced with
180            the new version (.999375-10).
181    
182            * tests/Simple.R: regression test for the bugs.
183    
184    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/sparseVector.R (spV2M): fix for "isparseVector".
187            Further, fix <diag> -> <sparseVector> coercion
188            (repSpV): add rep(<sparseVector>, .) method
189    
190            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
191            use as.vector(.).
192    
193            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
194    
195            * R/AllClass.R: new (hidden) class union "scarceMatrix"
196            * R/AllClass.R: sparseVector: add prototype
197    
198            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
199            Kasper Kristensen
200    
201    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * tests/other-pkgs.R: add more interesting Matrix -> graph
204    
205    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
208            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
209    
210    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * DESCRIPTION: release 0.999375-10 to CRAN
213    
214            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
215            .bdiag().
216            * man/bdiag.Rd: update, including test.
217    
218    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * tests/Simple.R: add minimal bdiag() checks
221    
222            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
223              factor out the Tsparse - internal computation into new .bdiag()
224    
225    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/nsparseMatrix.R: specific fast all() and any() methods.
228    
229            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
230            when trying to produce too large result.
231    
232            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
233            very large matrices.
234    
235            * R/sparseMatrix.R (printSpMatrix2): new function, used by
236            show(<sparseMatrix>).
237    
238            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
239    
240    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * src/Mutils.c (m_encodeInd, m_encodeInd2):
243            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
244    
245            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
246            big matrices): -> 2nd argument 'di' instead of 'nr' !
247    
248    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/dtCMatrix.R: faster dgC* -> dtC* method
251            * tests/Simple.R: (hence removed "FIXME")
252    
253            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
254            which can be be turned off for possible speed gains.
255    
256    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
259    
260            * R/not.R: fix !<ldiMatrix>
261            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
262    
263            * R/diagMatrix.R (Ops): fix one-off thinko in
264            <diagonal> o <numeric> methods
265    
266            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
267    
268    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
271            * tests/Simple.R: testing the above
272    
273    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
276    
277    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
280            * NAMESPACE (unname): finally exported
281    
282    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/Auxiliaries.R (cholMat): possibly keep packed
285    
286            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
287            for R < 2.7.0.
288    
289            * R/Tsparse.R ([): for triangularMatrix, check if result may be
290            triangular.
291            * tests/indexing.R: regression test
292    
293    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
296            * R/Ops.R: more methods, for lMatrix/nMatrix
297    
298    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * R/expm.R: new file for all expm() methods; notably new ones for
301            diagonal*, triangular*, symmetric* and also simple "matrix".
302    
303    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
306    
307            * inst/test-tools.R (assert.EQ.mat): better message when not equal
308    
309            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
310    
311            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
312            [dl]denseMatrix {identical slots; but more logical method dispatch}
313    
314    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
317    
318            * R/diagMatrix.R (determinant): method
319    
320    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
323    
324            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
325    
326            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
327            its diagonal
328    
329    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
332    
333            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
334    
335            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
336    
337            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
338    
339    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
342    
343            * R/Ops.R (.do.Logic.lsparse): fix NA case
344    
345            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
346    
347            * R/Auxiliaries.R (nnzero): fix special cases, using
348            * R/Auxiliaries.R (indDiag): new utility
349            * R/Auxiliaries.R (indTri): new argument 'diag'
350    
351            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
352    
353    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
356    
357            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
358            ".tCMatrix" triangular matrix.
359    
360            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
361            'clx' can be class *or* class representation.
362            (nnzSparse): new.
363            (non0ind): new 'xtendSymm' argument; used in
364            * R/Ops.R:
365    
366            * R/pMatrix.R: more efficient determinant() method
367    
368    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
371            * [disactivated] NAMESPACE: export(det)
372    
373            * R/diagMatrix.R (mkDiag): new substitute for diag()
374    
375            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
376            (as0, as1): new utility.
377    
378            * R/Csparse.R (diag, band): need diagU2N()
379    
380            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
381    
382            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
383    
384            * R/Ops.R (Compare): fix <nsp> o <nsp> case
385    
386            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
387    
388    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/Auxiliaries.R (signPerm): new utility for
391            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
392    
393            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
394            since we have our own error handler (and can use tryCatch() from R).
395    
396    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
399    
400            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
401            when not positive definite.
402    
403            * R/Auxiliaries.R (asTri): new auxiliary
404            (non0.i): make *much* faster for Tsparse with many non-zero
405            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
406    
407            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
408            test-tools.R , see below
409    
410            * R/dMatrix.R: fix "Summary" method: + diagU2N()
411    
412            * NAMESPACE, R/Matrix.R: add mean() method
413    
414    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
417            cold-hot colors; try *changed* default useAbs = FALSE
418            * man/image-methods.Rd:  nice examples
419    
420    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * inst/test-tools.R (checkMatrix): new function for modularizing part
423            of tstMatrixClass() in tests/Class+Meth.R
424    
425            * R/dsCMatrix.R: coercion from "matrix"
426            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
427    
428            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
429            add test for as(matrix(,0,0), <class>)
430    
431    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
434            work as determinant(matrix(,0,0)).
435    
436            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
437            * man/sparseLU-class.Rd: ditto
438    
439            * R/dgCMatrix.R (determinant): method building on lu()
440            * R/sparseMatrix.R, Matrix.R, ...: ditto
441    
442            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
443    
444    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
447            pattern matrices.
448    
449    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * src/dense.c (dense_to_Csparse): all declarations *before*
452            R_CheckStack(); needed e.g. for ancient gcc 2.96.
453    
454    
455    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * DESCRIPTION (Version): 0.999375-9 --- need to release
458            for R-devel (and R 2.7.0 alpha soon).
459    
460            * R/AllClass.R: drop "double" from "atomicVector" class union
461    
462            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
463            * R/dgeMatrix.R: ditto
464    
465            * R/sparseMatrix.R (summary): count NAs
466    
467            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
468    
469    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
472            order to become compatible to new R 2.7.0 base::rcond().
473    
474    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
477    
478            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
479    
480            * inst/test-tools.R (isValid): new utility, used much in
481            * tests/simple.R:
482    
483            * man/BunchKaufman-methods.Rd: added too
484    
485    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * R/dsyMatrix.R: add BunchKaufman() methods.
488            * R/dspMatrix.R:
489    
490            * src/init.c: add dsyMatrix_trf
491    
492    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
493    
494            * DESCRIPTION (Version): release 0.999375-7
495            * src/CHMfactor.c (CHMfactor_update): fix
496    
497    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
500            internal_chm_factor().
501    
502            * R/AllGeneric.R: do *not* define a "chol" generic
503                    (but rather use the implicit one *without* making pivot
504                    part of the signature)
505            * R/*.R: drop the 'pivot' from chol's signature and make
506                    'pivot=FALSE' a default argument of method definitions.
507    
508            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
509            version of Matrix
510    
511    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
514    
515            * R/sparseMatrix.R (is.na): new simple method
516            * R/denseMatrix.R (is.na): ditto.
517    
518            * R/diagMatrix.R (.symDiagonal): newly exported utility.
519    
520            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
521    
522            * src/UFsparse_download.sh: -->
523            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
524    
525    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
528            functionality; barely tested in
529            * tests/factorizing.R
530    
531            * src/Csparse.c (diag_tC): new functionality to enable faster
532            determinant(<dsCMatrix>, .) in
533            * R/dsCMatrix.R
534    
535    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
536    
537            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
538              src/CHMfactor.c, src/CHMfactor.h,
539              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
540              Log-determinant of the parent matrix from a CHMfactor object as
541              chm_factor_ldetL2; documentation and support
542    
543    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
546    
547    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
550            warning.
551    
552    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
555    
556            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
557              <diagonal> o <sparse_triangular>
558              setAs(., "nMatrix") added.
559    
560            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
561    
562            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
563                    new argument 'checkDense = FALSE'.
564    
565    
566    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
569            back-permutation of the matrix exponential.
570    
571            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
572    
573            * DESCRIPTION (Date,Version): ready to release 0.999375-5
574    
575            * tests/simple.R: testing diagN2U
576    
577    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * R/Auxiliaries.R (diagN2U): interface to
580    
581            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
582    
583            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
584    
585    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * src/chm_common.c (chm_diagN2U): new utility.
588    
589            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
590            make use of chm_diagN2U() and hence now preserve triangularity and
591            unit-triangularity.
592    
593            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
594    
595    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
596    
597            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
598    
599            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
600            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
601    
602            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
603    
604            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
605    
606            * src/chm_common.c (AS_CHM_FINISH): add note about problem
607            for triangular (diag = "U").
608    
609    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
612            * R/bind.R:  .Call(dense_to_Csparse, *)
613    
614    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * R/Matrix.R (Matrix): no longer use coercions to specific classes
617                    (since we are discouraging them in user code).
618    
619            * tests/*.R: also replaces coercions to specific classes by
620            coercions to super classes.
621    
622            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
623    
624    
625    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
626    
627            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
628    
629            * src/dense.c (dense_band): generalized from ddense_band
630    
631            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
632              now for "denseMatrix" (instead of just "ddense*"); much
633              simplified setMethod()s for these.
634    
635            * src/dense.c (dense_to_symmetric): generalized from ddense_*
636    
637    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
638    
639            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
640            version of as(*, "symmetricMatric").
641    
642            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
643            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
644    
645    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
646    
647            * R/Matrix.R (subset.ij): utility, as first step to faster
648               M [ <ij-matrix> ] indexing.
649    
650            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
651    
652            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
653            for more efficient symmpart() and skewpart() methods.
654    
655            * src/Mutils.c (equal_string_vectors): utility
656    
657            * src/dense.c (ddense_to_symmetric): new function used in
658    
659            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
660    
661            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
662            order to match the generic (and evade .local(..)).
663    
664            * R/dsCMatrix.R: dgC -> dsC: use C code!
665    
666            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
667            as per TODO
668    
669            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
670    
671            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
672    
673    
674    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
675    
676            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
677    
678            * R/Auxiliaries.R (non0.i): take out of non0ind
679    
680            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
681            make tril(), triu(), band() work for "matrix" and all "dense*"
682    
683            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
684            * tests/simple.R: test the fix above
685    
686            * R/sparseMatrix.R ([): simplification: no coerce to <general>
687                    before we use as(., <Tsparse>)[...] anyway
688    
689            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
690    
691            * R/triangularMatrix.R (isTriangular): methods for all subclasses
692            instead of "triangularMatrix" -- just to disambiguate
693    
694    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
695    
696            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
697            * tests/indexing.R: example that fails above
698    
699    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
700    
701            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
702            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
703                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
704    
705            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
706            * src/Tsparse.h, init.c: ditto
707            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
708                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
709            * R/sparseMatrix.R (isTriangular): hence simplified
710    
711    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
712    
713            * R/Ops.R (.Arith.Csparse): new utility factored out of former
714              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
715    
716    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
717    
718            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
719    
720            * inst/test-tools.R (isOrthogonal): new function; also file restructured
721    
722    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
725            coercion to "nMatrix" and "pMatrix"
726    
727            * R/AllClass.R: "Schur" class;  "number" class union
728            * man/number-class.Rd:
729            * man/Schur-class.Rd:
730    
731            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
732            (.simpleSchur): Schur() method for diagonal matrices
733            (.triSchur):    Schur() method for triangular matrices
734            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
735    
736    
737    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
740    
741    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
744                    in order to ensure 'system = *' is not lost;
745                    formals()$system instead of cut&paste.
746            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
747    
748    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
749    
750            * DESCRIPTION (Date): make ready for release --> 0.999375-4
751    
752            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
753    
754    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
755    
756            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
757                    and hence does as.vector(.).
758            * man/pMatrix-class.Rd: docs
759            * R/sparseMatrix.R: fix for printing "integer sparse"
760    
761            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
762    
763            * R/Matrix.R and others: use "exact" function argument list for
764                    both "["   : (x, i,j, ..., drop)
765                    and  "[<-" : (x, i,j, ..., value)
766    
767            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
768            * R/Tsparse.R (replTmat):    ditto
769            * R/diagMatrix.R (replDiag): ditto
770            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
771            * tests/indexing.R: testing the above
772    
773    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * R/sparseMatrix.R (cov2cor): method for sparse matrices
776    
777            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
778    
779            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
780    
781            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
782    
783    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
784    
785            * R/Matrix.R: "generic" cov2cor() method
786    
787            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
788                    speed up Q %*% D %*% t(Q)
789            * tests/dpoMatrix.R: test nearPD()
790    
791    2007-12-05  Doug Bates and Martin Maechler
792    
793            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
794            stats::xtabs() allowing to create sparse matrices.
795    
796    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
797    
798            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
799    
800    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
801    
802            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
803    
804    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
805    
806            * R/LU.R: solve() method for "denseLU"
807    
808    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
809    
810            * DESCRIPTION (Version): 0.999375-3 preparing for release
811    
812            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
813    
814            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
815    
816    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
817    
818            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
819              thanks to Kasper Kristensen.
820            * tests/matprod.R: regression test for that.
821    
822    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
823    
824            * [r4778] R/AllGeneric.R: Check R version before defining generics for
825              primitives
826    
827    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
828    
829            * R/denseMatrix.R (rcond): method
830            * R/sparseQR.R (rcond): method, use x or t(x)
831    
832    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
833    
834            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
835            matrices.
836            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
837    
838            * man/rcond.Rd: mention the more general definition, and add
839            example for non-square matrices.
840    
841            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
842    
843    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
844    
845            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
846    
847    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
848    
849            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
850            * tests/indexing.R: add new regression for the above cases.
851    
852    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
853    
854            * src/Mutils.h (__sun): clause for alloca.h on Solaris
855    
856    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
857    
858            * DESCRIPTION (Date, Version): 0.999375-2
859    
860    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
861    
862            * R/HBMM.R (readMM): make work for pattern matrices as well
863    
864    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
865    
866            * [r4730] src/Mutils.h: declare alloca
867            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
868              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
869              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
870              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
871              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
872              methods; switch writeMM to use CHOLMOD code; repair readMM
873    
874    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
875    
876            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
877            Oehlschlaegel's ... result type still to be discussed!
878    
879    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
880    
881            * man/image-methods.Rd: new, combining all image() methods
882    
883    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
884    
885            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
886            to work via dgC...
887    
888            * R/Matrix.R (Matrix): special treatment for "table" (S3)
889    
890    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
891    
892            * R/dgTMatrix.R (image): change defaults to
893                    aspect = "iso", colorkey = FALSE
894    
895    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
898            must copy its *expanded* x slot before LAPACK call.
899    
900            * tests/matprod.R: test the last days' changes.
901    
902    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
903    
904            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
905              as well as in sources
906            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
907              Lapack call
908    
909    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
910    
911            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
912                    ("Matrix", "matrix") which is needed in some cases.
913            Ditto for solve().
914    
915            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
916            infinite recursion in dispatch for some cases.
917    
918    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
919    
920            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
921              so pointers match
922    
923    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
924    
925            * DESCRIPTION (Date): set ready for release -- 0.999375-1
926    
927    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
928    
929            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
930              src/chm_common.c, src/chm_common.h: Change API for
931              numeric_as_chm_dense and N_AS_CHM_DN
932    
933    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
934    
935            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
936            * tests/matprod.R: regr.test for it
937    
938    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
939    
940            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
941            * tests/group-methods.R: and regression-test it
942    
943    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
944    
945            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
946              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
947              triplet_to_sparse, documentation, use typedefs
948    
949    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
950    
951            * man/dpoMatrix-class.Rd: added 'corMatrix' example
952    
953            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
954            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
955            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
956    
957            * R/lsparseMatrix.R: bug fix in "all" method
958            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
959    
960            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
961            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
962                    + matrix |-> nMatrix coercion
963            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
964            * man/pMatrix-class.Rd: ditto
965    
966            * R/Matrix.R (Summary): method for non-dMatrix
967    
968            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
969            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
970                    test all Summary methods.
971    
972    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
973    
974            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
975    
976    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
977    
978            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
979    
980            * R/pMatrix.R (t?crossprod): methods for pMatrix
981    
982    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
983    
984            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
985    
986    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
987    
988            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
989              trying to fix a subtle bug - which has been somewhere else.
990    
991    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
992    
993            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
994              solve the bug
995    
996    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
997    
998            * src/dgCMatrix.c (compressed_to_TMatrix):
999    
1000    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1001    
1002            * src/Csparse.c (Rsparse_validate): new, to have some validity
1003            checking for RsparseMatrix
1004            * src/dgCMatrix.c (xRMatrix_validate): ditto
1005            * src/dtCMatrix.c (tRMatrix_validate): ditto
1006    
1007    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
1008    
1009            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
1010              lgRMatrix
1011            * [r4568] DESCRIPTION: Prepare for bug-fix release
1012            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
1013              for declaration of cholmod_symmetry
1014    
1015    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1016    
1017            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
1018            release.
1019    
1020    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
1021    
1022            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
1023              functions - no longer used
1024            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
1025              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
1026              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
1027              Alloca
1028    
1029    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
1030    
1031            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
1032              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
1033              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
1034              src/t_gCMatrix_colSums.c: more R_CheckStack()s
1035    
1036    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
1037    
1038            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
1039              the required amount of memory then call M_numeric_as_chm_dense.
1040            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
1041              (like Calloc but calling alloca)
1042    
1043    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1044    
1045            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
1046            and extended with more sophisticated 'col.names' option.
1047            * NAMESPACE: export  printSparseMatrix()
1048            * man/printSpMatrix.Rd: document, incl. examples
1049    
1050    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
1051    
1052            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
1053              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
1054              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
1055    
1056    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1057    
1058            * DESCRIPTION (Version): 0.99875-4
1059    
1060            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
1061            some dimnames perservation.
1062    
1063            * R/dsTMatrix.R (t-method): keep dimnames
1064            * R/dtTMatrix.R:  ditto
1065    
1066            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
1067            and ncol(.) < 10
1068    
1069            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
1070            from Mutils.h
1071    
1072            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
1073            e.g. in as(<ngCMatrix>, "matrix")
1074    
1075    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
1076    
1077            * [r4529] .: Create a branch for the API changes from the 0.99875
1078              series to the 0.999375 series
1079            * [r4530] DESCRIPTION, inst/include/Matrix.h,
1080              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
1081              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
1082              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
1083              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
1084              as_cholmod_x functions
1085    
1086    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
1087    
1088            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
1089              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
1090              to Comparisons
1091    
1092    >>>>>>> .merge-right.r4561
1093    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1094    
1095            * DESCRIPTION (Version): 0.99875-3 ready to be released.
1096    
1097            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
1098    
1099            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
1100            that should also work in a future version of R.
1101    
1102    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1103    
1104            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
1105    
1106            * R/sparseVector.R: more *sparseVector coercions, notably for
1107            non - double ones.
1108    
1109    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1110    
1111            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
1112              notably the new ones building on the new .Call(.)s:
1113    
1114            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
1115            all 4 of [dlin]gCMatrix_colSums().
1116    
1117    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
1118    
1119            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
1120            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
1121              result
1122    
1123    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1124    
1125            * R/kronecker.R: fix typo (could lead to inf.recursion)
1126            * test/simple.R: testing that
1127    
1128            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
1129            method as well (which can have arguments, show() can't).
1130    
1131    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
1132    
1133            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
1134              added dgCMatrix_colSums for [col,row][Sums,Means]
1135    
1136    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
1137    
1138            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
1139              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
1140              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
1141            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
1142              class
1143            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
1144              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
1145              row names to store the levels - duh!  Added an example.
1146    
1147    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1148    
1149            * src/Csparse.c (Csparse_validate): check for *repeated* entries
1150            thanks to example from Christian Buchta; with a test here:
1151            * tests/simple.R:
1152    
1153    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1154    
1155            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
1156            of colSums(*, sparseResult = TRUE)
1157    
1158    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1159    
1160            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
1161            'na.rm = FALSE' as "everywhere" else in R.
1162    
1163    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
1164    
1165            * [r4421] src/CSparse_install.sh: Modify for new organization of
1166              CSparse package
1167            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
1168              SuiteSparse
1169            * [r4426] src/Makefile: add ./UFconfig to the include path for
1170              compilation
1171            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
1172            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
1173              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
1174    
1175    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1176    
1177            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
1178            * R/sparseMatrix.R (prSpMatrix): now gives a message about
1179            suppressed column names.
1180    
1181    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
1182    
1183            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
1184              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
1185              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
1186              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
1187              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
1188              Remove warnings after change to const char* CHAR
1189    
1190    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
1191    
1192            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
1193              type of M_cholmod_ssmult
1194    
1195    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
1196    
1197            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
1198              src/init.c: Yet another cholmod export - cholmod_ssmult
1199    
1200    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1201    
1202            * NAMESPACE: exported drop0(), since
1203            * man/drop0.Rd: I have seen several cases, I really wanted to use
1204            it, so our users may want too.
1205    
1206    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1207    
1208            * man/colSums.Rd: separately document colSums() etc, since these
1209            have the extra argument 'sparseResult'.
1210    
1211    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1212    
1213            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
1214            * man/spMatrix.Rd: docu., including examples
1215    
1216            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
1217            in order to make colMeans() etc fast *and* correct.
1218            * R/sparseVector.R (replSPvec): "[<-" functionality for
1219            sparseVectors; tested in
1220            * tests/simple.R:
1221    
1222    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1223    
1224            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1225            (very) sparse Matrices; output similar to Matlab's print().
1226    
1227    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
1228    
1229            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
1230            0-based, indices (Jose Quesada <quesada@gmail.com>).
1231    
1232    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
1233    
1234            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
1235    
1236    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1237    
1238            * R/Auxiliaries.R (sparsapply): new utility, much faster than
1239            tapply1() for large sparse matrices.
1240    
1241    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1242    
1243            * R/Matrix.R (dim<-): reshape now via sparseVector.
1244    
1245            * R/sparseVector.R: methods and function for
1246            * R/AllClass.R: new "sparseVector" class and daughters.
1247            * NAMESPACE: export new classes
1248    
1249    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1250    
1251            * DESCRIPTION (Version): 0.99875-1
1252            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1253    
1254    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1255    
1256            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1257            indexing
1258            * tests/indexing.R: test set for that.
1259    
1260    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1261    
1262            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1263            entries.
1264            * tests/indexing.R(out): add regression test for it
1265    
1266    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1267    
1268            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1269            name for "!" method definitions.
1270    
1271    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1272    
1273            * R/Tsparse.R (intI): new utility, used for "[" :
1274                    Cleanup up there, and fixes for duplicated indices - more TODO!
1275    
1276            * tests/indexing.R(out): more tests
1277    
1278  2007-04-25  Douglas Bates  <bates@stat.wisc.edu>  2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1279    
1280          * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack          * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
# Line 6  Line 1283 
1283          * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export          * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1284          cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).          cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1285    
1286    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1287    
1288            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1289    
1290    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1291    
1292            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1293            up with extraneous names '0'...'<n-1>'
1294    
1295  2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1296    
1297          * R/dgTMatrix.R (mat2dgT): care about NAs          * R/dgTMatrix.R (mat2dgT): care about NAs

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