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revision 2043, Sat Aug 11 03:18:26 2007 UTC revision 2250, Thu Aug 28 11:54:53 2008 UTC
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1    2008-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Ops.R (Compare(<Csparse>,<Csparse>): fix for nsparseMatrix
4    
5    2008-08-27  Douglas Bates <bates@stat.wisc.edu>
6    
7            * R/sparseMatrix.R: fac2sparse() for NA's
8    
9    2008-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/sparseVector.R (all.equal.sparseV): make work for nsparseVector's
12    
13    2008-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * src/dgCMatrix.c (dgCMatrix_LU): partially revert change
16            r2175 (2008-04-23) and do give an error for a singular matrix.
17            * man/lu.Rd, R/Auxiliaries.R (detSparseLU): adapt to that.
18    
19            * R/LU.R: expand( <sparseLU> )
20    
21            * NAMESPACE, man/all.equal-methods.Rd:
22            * R/Matrix.R (all.equal): methods for Matrices,
23            * R/sparseMatrix.R, R/sparseVector.R: sparseMatrices and -Vectors
24    
25    
26    2008-08-23  Douglas Bates <bates@stat.wisc.edu>
27    
28            * [r2243] R/CHMfactor.R, man/CHMfactor-class.Rd: Added expand method and
29              documentation for CHMfactor class
30            * [r2241] R/CHMfactor.R: Added trivial coercion method for CHMfactor ->
31              pMatrix
32    
33    2008-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/nsCMatrix.R (setAs(., dgTMatrix))): remove unused method
36    
37    2008-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/Ops.R (.Ops2dge.via.x, and many others): eliminate never-used
40            variable assignments {from "next version" codetools}.
41            * R/Csparse.R, R/Tsparse.R: ditto
42    
43    2008-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/sparseVector.R (sp2vec, coerce to sparseVector):
46            make sure no integer overflows happen, and use double precision
47            (n, index) where appropriate.
48    
49            * tests/Simple.R: test "large" sparse vectors.
50    
51    2008-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/AllClass.R (sparseVector): 'length' and 'i' are "numeric", not
54            just integer (allowing much longer length).
55    
56    2008-07-28  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/AllClass.R (diagonalMatrix): extend  "sparseMatrix" instead of
59            "denseMatrix".  This renders "scarceMatrix" dispensable and
60            invalidates part of MM's presentations on "space of Matrix
61            classes", but seems cleaner overall.
62    
63            * R/diagMatrix.R, etc: eliminate "scarceMatrix", replacing it by
64            "sparseMatrix" in method signatures;
65            further, instead of coercing to "sparseMatrix", coerce to
66            "TsparseMatrix" now.
67    
68    2008-07-26  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * src/dgCMatrix.c (dgCMatrix_qrsol): allow third argument 'order' in
71            .Call(.)
72            * R/sparseMatrix.R (lm.fit.sparse), src/dgCMatrix.h, src/init.c: ditto
73    
74    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
77            recursion in new test in
78            * tests/matprod.R: testing the above and another solve() case, below
79    
80            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
81            e.g. triangular 'x'.
82    
83            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
84            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
85            correctly with unit-triangular x
86    
87            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
88            instead of not checking diagU.
89    
90            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
91            experiments where diagonalMatrix would extend sparse*.
92    
93    
94    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
97            "x@p[ncol(x)]" instead of length(x@i).
98            * R/Auxiliaries.R (nnzero): ditto
99    
100            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
101            since that fails for over-allocated i.
102    
103            * tests/validObj.R: more testing of over-allocated (i,x) slots
104    
105    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
108            'sort_in_place' and set it to TRUE in call from
109            * src/Csparse.c (Csparse_validate): sort in place, making sure that
110            validObject() continues sort the columns if needed.
111    
112            * tests/validObj.R: now tests that more thoroughly, and
113            * man/CsparseMatrix-class.Rd: documents it.
114    
115    2008-07-22  Douglas Bates <bates@stat.wisc.edu>
116    
117            * [r2233] src/chm_common.c: sort columns more carefully in
118              as_cholmod_sparse
119            * [r2231] src/chm_common.c: check for sorted columns in
120              as_cholmod_sparse instead of assuming it
121            * [r2228] src/cs_utils.c: Use R_alloc for semi-permanent storage when
122              expanding diagonal
123    
124    
125    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
128            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
129            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
130            diagU2N().
131    
132            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
133            .spDiagonal() and new .trDiagonal().
134    
135            * R/dtCMatrix.R (solve): make use of .trDiagonal()
136    
137    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
140            stumbled upon by Michael H.
141    
142            * tests/validObj.R: testing the bug-fix
143    
144            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
145            versions.
146    
147            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
148            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
149    
150            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
151              AS_CHM_SP() which includes diagU2N.
152    
153            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
154            adapt to 3 arguments.
155    
156    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
157    
158            * [r2220] src/dtCMatrix.c: Correct number of columns for rhs in
159              dtCMatrix_sparse_solve
160            * [r2219] src/cs_utils.c: eye->nz should be -1 for compressed column
161              storage
162            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
163              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
164              new solve method
165            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
166              Csparse_diagU2N functionality into Matrix_as_cs
167    
168    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
171    
172    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
173    
174            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
175              argument with default TRUE
176            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
177              Csparse_diagU2N
178            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
179              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
180              parent array; new solve method for signature(a = "dtCMatrix", b =
181              "sparseMatrix")
182    
183    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/diagMatrix.R (.bdiag): also keep result triangular
186    
187    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
188    
189            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
190              messages
191    
192    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
195            symmetric- or nsparse-Matrix, also fixing the bug introduced with
196            the new version (.999375-10).
197    
198            * tests/Simple.R: regression test for the bugs.
199    
200    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/sparseVector.R (spV2M): fix for "isparseVector".
203            Further, fix <diag> -> <sparseVector> coercion
204            (repSpV): add rep(<sparseVector>, .) method
205    
206            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
207            use as.vector(.).
208    
209            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
210    
211            * R/AllClass.R: new (hidden) class union "scarceMatrix"
212            * R/AllClass.R: sparseVector: add prototype
213    
214            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
215            Kasper Kristensen
216    
217    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * tests/other-pkgs.R: add more interesting Matrix -> graph
220    
221    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
224            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
225    
226    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * DESCRIPTION: release 0.999375-10 to CRAN
229    
230            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
231            .bdiag().
232            * man/bdiag.Rd: update, including test.
233    
234    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * tests/Simple.R: add minimal bdiag() checks
237    
238            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
239              factor out the Tsparse - internal computation into new .bdiag()
240    
241    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/nsparseMatrix.R: specific fast all() and any() methods.
244    
245            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
246            when trying to produce too large result.
247    
248            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
249            very large matrices.
250    
251            * R/sparseMatrix.R (printSpMatrix2): new function, used by
252            show(<sparseMatrix>).
253    
254            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
255    
256    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * src/Mutils.c (m_encodeInd, m_encodeInd2):
259            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
260    
261            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
262            big matrices): -> 2nd argument 'di' instead of 'nr' !
263    
264    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/dtCMatrix.R: faster dgC* -> dtC* method
267            * tests/Simple.R: (hence removed "FIXME")
268    
269            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
270            which can be be turned off for possible speed gains.
271    
272    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
275    
276            * R/not.R: fix !<ldiMatrix>
277            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
278    
279            * R/diagMatrix.R (Ops): fix one-off thinko in
280            <diagonal> o <numeric> methods
281    
282            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
283    
284    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
287            * tests/Simple.R: testing the above
288    
289    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
292    
293    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
296            * NAMESPACE (unname): finally exported
297    
298    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * R/Auxiliaries.R (cholMat): possibly keep packed
301    
302            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
303            for R < 2.7.0.
304    
305            * R/Tsparse.R ([): for triangularMatrix, check if result may be
306            triangular.
307            * tests/indexing.R: regression test
308    
309    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
312            * R/Ops.R: more methods, for lMatrix/nMatrix
313    
314    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/expm.R: new file for all expm() methods; notably new ones for
317            diagonal*, triangular*, symmetric* and also simple "matrix".
318    
319    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
322    
323            * inst/test-tools.R (assert.EQ.mat): better message when not equal
324    
325            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
326    
327            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
328            [dl]denseMatrix {identical slots; but more logical method dispatch}
329    
330    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
333    
334            * R/diagMatrix.R (determinant): method
335    
336    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
339    
340            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
341    
342            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
343            its diagonal
344    
345    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
348    
349            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
350    
351            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
352    
353            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
354    
355    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
358    
359            * R/Ops.R (.do.Logic.lsparse): fix NA case
360    
361            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
362    
363            * R/Auxiliaries.R (nnzero): fix special cases, using
364            * R/Auxiliaries.R (indDiag): new utility
365            * R/Auxiliaries.R (indTri): new argument 'diag'
366    
367            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
368    
369    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
372    
373            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
374            ".tCMatrix" triangular matrix.
375    
376            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
377            'clx' can be class *or* class representation.
378            (nnzSparse): new.
379            (non0ind): new 'xtendSymm' argument; used in
380            * R/Ops.R:
381    
382            * R/pMatrix.R: more efficient determinant() method
383    
384    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
387            * [disactivated] NAMESPACE: export(det)
388    
389            * R/diagMatrix.R (mkDiag): new substitute for diag()
390    
391            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
392            (as0, as1): new utility.
393    
394            * R/Csparse.R (diag, band): need diagU2N()
395    
396            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
397    
398            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
399    
400            * R/Ops.R (Compare): fix <nsp> o <nsp> case
401    
402            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
403    
404    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * R/Auxiliaries.R (signPerm): new utility for
407            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
408    
409            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
410            since we have our own error handler (and can use tryCatch() from R).
411    
412    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
415    
416            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
417            when not positive definite.
418    
419            * R/Auxiliaries.R (asTri): new auxiliary
420            (non0.i): make *much* faster for Tsparse with many non-zero
421            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
422    
423            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
424            test-tools.R , see below
425    
426            * R/dMatrix.R: fix "Summary" method: + diagU2N()
427    
428            * NAMESPACE, R/Matrix.R: add mean() method
429    
430    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
433            cold-hot colors; try *changed* default useAbs = FALSE
434            * man/image-methods.Rd:  nice examples
435    
436    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * inst/test-tools.R (checkMatrix): new function for modularizing part
439            of tstMatrixClass() in tests/Class+Meth.R
440    
441            * R/dsCMatrix.R: coercion from "matrix"
442            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
443    
444            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
445            add test for as(matrix(,0,0), <class>)
446    
447    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
450            work as determinant(matrix(,0,0)).
451    
452            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
453            * man/sparseLU-class.Rd: ditto
454    
455            * R/dgCMatrix.R (determinant): method building on lu()
456            * R/sparseMatrix.R, Matrix.R, ...: ditto
457    
458            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
459    
460    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
463            pattern matrices.
464    
465    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * src/dense.c (dense_to_Csparse): all declarations *before*
468            R_CheckStack(); needed e.g. for ancient gcc 2.96.
469    
470    
471    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
472    
473            * DESCRIPTION (Version): 0.999375-9 --- need to release
474            for R-devel (and R 2.7.0 alpha soon).
475    
476            * R/AllClass.R: drop "double" from "atomicVector" class union
477    
478            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
479            * R/dgeMatrix.R: ditto
480    
481            * R/sparseMatrix.R (summary): count NAs
482    
483            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
484    
485    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
488            order to become compatible to new R 2.7.0 base::rcond().
489    
490    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
493    
494            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
495    
496            * inst/test-tools.R (isValid): new utility, used much in
497            * tests/simple.R:
498    
499            * man/BunchKaufman-methods.Rd: added too
500    
501    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
502    
503            * R/dsyMatrix.R: add BunchKaufman() methods.
504            * R/dspMatrix.R:
505    
506            * src/init.c: add dsyMatrix_trf
507    
508    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
509    
510            * DESCRIPTION (Version): release 0.999375-7
511            * src/CHMfactor.c (CHMfactor_update): fix
512    
513    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
516            internal_chm_factor().
517    
518            * R/AllGeneric.R: do *not* define a "chol" generic
519                    (but rather use the implicit one *without* making pivot
520                    part of the signature)
521            * R/*.R: drop the 'pivot' from chol's signature and make
522                    'pivot=FALSE' a default argument of method definitions.
523    
524            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
525            version of Matrix
526    
527    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
530    
531            * R/sparseMatrix.R (is.na): new simple method
532            * R/denseMatrix.R (is.na): ditto.
533    
534            * R/diagMatrix.R (.symDiagonal): newly exported utility.
535    
536            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
537    
538            * src/UFsparse_download.sh: -->
539            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
540    
541    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
542    
543            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
544            functionality; barely tested in
545            * tests/factorizing.R
546    
547            * src/Csparse.c (diag_tC): new functionality to enable faster
548            determinant(<dsCMatrix>, .) in
549            * R/dsCMatrix.R
550    
551    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
552    
553            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
554              src/CHMfactor.c, src/CHMfactor.h,
555              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
556              Log-determinant of the parent matrix from a CHMfactor object as
557              chm_factor_ldetL2; documentation and support
558    
559    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
562    
563    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
566            warning.
567    
568    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
571    
572            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
573              <diagonal> o <sparse_triangular>
574              setAs(., "nMatrix") added.
575    
576            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
577    
578            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
579                    new argument 'checkDense = FALSE'.
580    
581    
582    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
585            back-permutation of the matrix exponential.
586    
587            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
588    
589            * DESCRIPTION (Date,Version): ready to release 0.999375-5
590    
591            * tests/simple.R: testing diagN2U
592    
593    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * R/Auxiliaries.R (diagN2U): interface to
596    
597            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
598    
599            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
600    
601    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * src/chm_common.c (chm_diagN2U): new utility.
604    
605            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
606            make use of chm_diagN2U() and hence now preserve triangularity and
607            unit-triangularity.
608    
609            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
610    
611    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
612    
613            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
614    
615            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
616            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
617    
618            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
619    
620            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
621    
622            * src/chm_common.c (AS_CHM_FINISH): add note about problem
623            for triangular (diag = "U").
624    
625    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
626    
627            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
628            * R/bind.R:  .Call(dense_to_Csparse, *)
629    
630    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * R/Matrix.R (Matrix): no longer use coercions to specific classes
633                    (since we are discouraging them in user code).
634    
635            * tests/*.R: also replaces coercions to specific classes by
636            coercions to super classes.
637    
638            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
639    
640    
641    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
644    
645            * src/dense.c (dense_band): generalized from ddense_band
646    
647            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
648              now for "denseMatrix" (instead of just "ddense*"); much
649              simplified setMethod()s for these.
650    
651            * src/dense.c (dense_to_symmetric): generalized from ddense_*
652    
653    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
654    
655            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
656            version of as(*, "symmetricMatric").
657    
658            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
659            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
660    
661    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
662    
663            * R/Matrix.R (subset.ij): utility, as first step to faster
664               M [ <ij-matrix> ] indexing.
665    
666            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
667    
668            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
669            for more efficient symmpart() and skewpart() methods.
670    
671            * src/Mutils.c (equal_string_vectors): utility
672    
673            * src/dense.c (ddense_to_symmetric): new function used in
674    
675            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
676    
677            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
678            order to match the generic (and evade .local(..)).
679    
680            * R/dsCMatrix.R: dgC -> dsC: use C code!
681    
682            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
683            as per TODO
684    
685            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
686    
687            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
688    
689    
690    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
693    
694            * R/Auxiliaries.R (non0.i): take out of non0ind
695    
696            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
697            make tril(), triu(), band() work for "matrix" and all "dense*"
698    
699            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
700            * tests/simple.R: test the fix above
701    
702            * R/sparseMatrix.R ([): simplification: no coerce to <general>
703                    before we use as(., <Tsparse>)[...] anyway
704    
705            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
706    
707            * R/triangularMatrix.R (isTriangular): methods for all subclasses
708            instead of "triangularMatrix" -- just to disambiguate
709    
710    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
711    
712            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
713            * tests/indexing.R: example that fails above
714    
715    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
718            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
719                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
720    
721            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
722            * src/Tsparse.h, init.c: ditto
723            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
724                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
725            * R/sparseMatrix.R (isTriangular): hence simplified
726    
727    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/Ops.R (.Arith.Csparse): new utility factored out of former
730              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
731    
732    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
735    
736            * inst/test-tools.R (isOrthogonal): new function; also file restructured
737    
738    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
739    
740            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
741            coercion to "nMatrix" and "pMatrix"
742    
743            * R/AllClass.R: "Schur" class;  "number" class union
744            * man/number-class.Rd:
745            * man/Schur-class.Rd:
746    
747            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
748            (.simpleSchur): Schur() method for diagonal matrices
749            (.triSchur):    Schur() method for triangular matrices
750            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
751    
752    
753    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
756    
757    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
760                    in order to ensure 'system = *' is not lost;
761                    formals()$system instead of cut&paste.
762            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
763    
764    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
765    
766            * DESCRIPTION (Date): make ready for release --> 0.999375-4
767    
768            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
769    
770    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
771    
772            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
773                    and hence does as.vector(.).
774            * man/pMatrix-class.Rd: docs
775            * R/sparseMatrix.R: fix for printing "integer sparse"
776    
777            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
778    
779            * R/Matrix.R and others: use "exact" function argument list for
780                    both "["   : (x, i,j, ..., drop)
781                    and  "[<-" : (x, i,j, ..., value)
782    
783            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
784            * R/Tsparse.R (replTmat):    ditto
785            * R/diagMatrix.R (replDiag): ditto
786            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
787            * tests/indexing.R: testing the above
788    
789    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * R/sparseMatrix.R (cov2cor): method for sparse matrices
792    
793            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
794    
795            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
796    
797            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
798    
799    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
800    
801            * R/Matrix.R: "generic" cov2cor() method
802    
803            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
804                    speed up Q %*% D %*% t(Q)
805            * tests/dpoMatrix.R: test nearPD()
806    
807    2007-12-05  Doug Bates and Martin Maechler
808    
809            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
810            stats::xtabs() allowing to create sparse matrices.
811    
812    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
813    
814            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
815    
816    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
817    
818            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
819    
820    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
821    
822            * R/LU.R: solve() method for "denseLU"
823    
824    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
825    
826            * DESCRIPTION (Version): 0.999375-3 preparing for release
827    
828            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
829    
830            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
831    
832    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
833    
834            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
835              thanks to Kasper Kristensen.
836            * tests/matprod.R: regression test for that.
837    
838    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
839    
840            * [r4778] R/AllGeneric.R: Check R version before defining generics for
841              primitives
842    
843    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
844    
845            * R/denseMatrix.R (rcond): method
846            * R/sparseQR.R (rcond): method, use x or t(x)
847    
848    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
849    
850            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
851            matrices.
852            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
853    
854            * man/rcond.Rd: mention the more general definition, and add
855            example for non-square matrices.
856    
857            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
858    
859    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
860    
861            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
862    
863    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
864    
865            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
866            * tests/indexing.R: add new regression for the above cases.
867    
868    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
869    
870            * src/Mutils.h (__sun): clause for alloca.h on Solaris
871    
872    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
873    
874            * DESCRIPTION (Date, Version): 0.999375-2
875    
876    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
877    
878            * R/HBMM.R (readMM): make work for pattern matrices as well
879    
880    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
881    
882            * [r4730] src/Mutils.h: declare alloca
883            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
884              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
885              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
886              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
887              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
888              methods; switch writeMM to use CHOLMOD code; repair readMM
889    
890    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
891    
892            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
893            Oehlschlaegel's ... result type still to be discussed!
894    
895  2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897          * man/image-methods.Rd: new, combining all image() methods          * man/image-methods.Rd: new, combining all image() methods
# Line 25  Line 919 
919    
920          * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs          * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
921            as well as in sources            as well as in sources
922            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
923              Lapack call
924    
925  2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
926    

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