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revision 1966, Sat Jul 7 20:07:58 2007 UTC revision 2154, Sat Mar 22 21:23:12 2008 UTC
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1  2007-07-07 18:23  Douglas Bates <bates@stat.wisc.edu>  2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
4            internal_chm_factor().
5    
6            * R/AllGeneric.R: do *not* define a "chol" generic
7                    (but rather use the implicit one *without* making pivot
8                    part of the signature)
9            * R/*.R: drop the 'pivot' from chol's signature and make
10                    'pivot=FALSE' a default argument of method definitions.
11    
12            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
13            version of Matrix
14    
15    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
18    
19            * R/sparseMatrix.R (is.na): new simple method
20            * R/denseMatrix.R (is.na): ditto.
21    
22            * R/diagMatrix.R (.symDiagonal): newly exported utility.
23    
24            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
25    
26            * src/UFsparse_download.sh: -->
27            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
28    
29    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
32            functionality; barely tested in
33            * tests/factorizing.R
34    
35            * src/Csparse.c (diag_tC): new functionality to enable faster
36            determinant(<dsCMatrix>, .) in
37            * R/dsCMatrix.R
38    
39    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
40    
41            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
42              src/CHMfactor.c, src/CHMfactor.h,
43              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
44              Log-determinant of the parent matrix from a CHMfactor object as
45              chm_factor_ldetL2; documentation and support
46    
47    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
50    
51    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
54            warning.
55    
56    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
59    
60            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
61              <diagonal> o <sparse_triangular>
62              setAs(., "nMatrix") added.
63    
64            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
65    
66            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
67                    new argument 'checkDense = FALSE'.
68    
69    
70    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
73            back-permutation of the matrix exponential.
74    
75            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
76    
77            * DESCRIPTION (Date,Version): ready to release 0.999375-5
78    
79            * tests/simple.R: testing diagN2U
80    
81    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/Auxiliaries.R (diagN2U): interface to
84    
85            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
86    
87            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
88    
89    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * src/chm_common.c (chm_diagN2U): new utility.
92    
93            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
94            make use of chm_diagN2U() and hence now preserve triangularity and
95            unit-triangularity.
96    
97            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
98    
99    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
102    
103            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
104            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
105    
106            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
107    
108            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
109    
110            * src/chm_common.c (AS_CHM_FINISH): add note about problem
111            for triangular (diag = "U").
112    
113    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
116            * R/bind.R:  .Call(dense_to_Csparse, *)
117    
118    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/Matrix.R (Matrix): no longer use coercions to specific classes
121                    (since we are discouraging them in user code).
122    
123            * tests/*.R: also replaces coercions to specific classes by
124            coercions to super classes.
125    
126            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
127    
128    
129    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
132    
133            * src/dense.c (dense_band): generalized from ddense_band
134    
135            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
136              now for "denseMatrix" (instead of just "ddense*"); much
137              simplified setMethod()s for these.
138    
139            * src/dense.c (dense_to_symmetric): generalized from ddense_*
140    
141    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
144            version of as(*, "symmetricMatric").
145    
146            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
147            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
148    
149    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/Matrix.R (subset.ij): utility, as first step to faster
152               M [ <ij-matrix> ] indexing.
153    
154            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
155    
156            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
157            for more efficient symmpart() and skewpart() methods.
158    
159            * src/Mutils.c (equal_string_vectors): utility
160    
161            * src/dense.c (ddense_to_symmetric): new function used in
162    
163            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
164    
165            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
166            order to match the generic (and evade .local(..)).
167    
168            * R/dsCMatrix.R: dgC -> dsC: use C code!
169    
170            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
171            as per TODO
172    
173            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
174    
175            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
176    
177    
178    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
181    
182            * R/Auxiliaries.R (non0.i): take out of non0ind
183    
184            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
185            make tril(), triu(), band() work for "matrix" and all "dense*"
186    
187            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
188            * tests/simple.R: test the fix above
189    
190            * R/sparseMatrix.R ([): simplification: no coerce to <general>
191                    before we use as(., <Tsparse>)[...] anyway
192    
193            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
194    
195            * R/triangularMatrix.R (isTriangular): methods for all subclasses
196            instead of "triangularMatrix" -- just to disambiguate
197    
198    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
201            * tests/indexing.R: example that fails above
202    
203    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
206            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
207                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
208    
209            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
210            * src/Tsparse.h, init.c: ditto
211            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
212                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
213            * R/sparseMatrix.R (isTriangular): hence simplified
214    
215    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * R/Ops.R (.Arith.Csparse): new utility factored out of former
218              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
219    
220    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
223    
224            * inst/test-tools.R (isOrthogonal): new function; also file restructured
225    
226    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
229            coercion to "nMatrix" and "pMatrix"
230    
231            * R/AllClass.R: "Schur" class;  "number" class union
232            * man/number-class.Rd:
233            * man/Schur-class.Rd:
234    
235            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
236            (.simpleSchur): Schur() method for diagonal matrices
237            (.triSchur):    Schur() method for triangular matrices
238            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
239    
240    
241    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
244    
245    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
248                    in order to ensure 'system = *' is not lost;
249                    formals()$system instead of cut&paste.
250            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
251    
252    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * DESCRIPTION (Date): make ready for release --> 0.999375-4
255    
256            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
257    
258    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
261                    and hence does as.vector(.).
262            * man/pMatrix-class.Rd: docs
263            * R/sparseMatrix.R: fix for printing "integer sparse"
264    
265            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
266    
267            * R/Matrix.R and others: use "exact" function argument list for
268                    both "["   : (x, i,j, ..., drop)
269                    and  "[<-" : (x, i,j, ..., value)
270    
271            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
272            * R/Tsparse.R (replTmat):    ditto
273            * R/diagMatrix.R (replDiag): ditto
274            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
275            * tests/indexing.R: testing the above
276    
277    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/sparseMatrix.R (cov2cor): method for sparse matrices
280    
281            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
282    
283            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
284    
285            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
286    
287    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/Matrix.R: "generic" cov2cor() method
290    
291            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
292                    speed up Q %*% D %*% t(Q)
293            * tests/dpoMatrix.R: test nearPD()
294    
295    2007-12-05  Doug Bates and Martin Maechler
296    
297            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
298            stats::xtabs() allowing to create sparse matrices.
299    
300    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
303    
304    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
307    
308    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/LU.R: solve() method for "denseLU"
311    
312    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * DESCRIPTION (Version): 0.999375-3 preparing for release
315    
316            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
317    
318            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
319    
320    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
323              thanks to Kasper Kristensen.
324            * tests/matprod.R: regression test for that.
325    
326    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
327    
328            * [r4778] R/AllGeneric.R: Check R version before defining generics for
329              primitives
330    
331    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * R/denseMatrix.R (rcond): method
334            * R/sparseQR.R (rcond): method, use x or t(x)
335    
336    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
339            matrices.
340            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
341    
342            * man/rcond.Rd: mention the more general definition, and add
343            example for non-square matrices.
344    
345            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
346    
347    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
350    
351    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
354            * tests/indexing.R: add new regression for the above cases.
355    
356    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * src/Mutils.h (__sun): clause for alloca.h on Solaris
359    
360    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * DESCRIPTION (Date, Version): 0.999375-2
363    
364    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/HBMM.R (readMM): make work for pattern matrices as well
367    
368    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
369    
370            * [r4730] src/Mutils.h: declare alloca
371            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
372              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
373              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
374              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
375              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
376              methods; switch writeMM to use CHOLMOD code; repair readMM
377    
378    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
381            Oehlschlaegel's ... result type still to be discussed!
382    
383    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * man/image-methods.Rd: new, combining all image() methods
386    
387    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
390            to work via dgC...
391    
392            * R/Matrix.R (Matrix): special treatment for "table" (S3)
393    
394    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * R/dgTMatrix.R (image): change defaults to
397                    aspect = "iso", colorkey = FALSE
398    
399    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
402            must copy its *expanded* x slot before LAPACK call.
403    
404            * tests/matprod.R: test the last days' changes.
405    
406    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
407    
408            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
409              as well as in sources
410            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
411              Lapack call
412    
413    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
416                    ("Matrix", "matrix") which is needed in some cases.
417            Ditto for solve().
418    
419            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
420            infinite recursion in dispatch for some cases.
421    
422    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
423    
424            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
425              so pointers match
426    
427    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * DESCRIPTION (Date): set ready for release -- 0.999375-1
430    
431    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
432    
433            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
434              src/chm_common.c, src/chm_common.h: Change API for
435              numeric_as_chm_dense and N_AS_CHM_DN
436    
437    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
438    
439            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
440            * tests/matprod.R: regr.test for it
441    
442    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
445            * tests/group-methods.R: and regression-test it
446    
447    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
448    
449            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
450              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
451              triplet_to_sparse, documentation, use typedefs
452    
453    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * man/dpoMatrix-class.Rd: added 'corMatrix' example
456    
457            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
458            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
459            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
460    
461            * R/lsparseMatrix.R: bug fix in "all" method
462            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
463    
464            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
465            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
466                    + matrix |-> nMatrix coercion
467            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
468            * man/pMatrix-class.Rd: ditto
469    
470            * R/Matrix.R (Summary): method for non-dMatrix
471    
472            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
473            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
474                    test all Summary methods.
475    
476    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
479    
480    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
483    
484            * R/pMatrix.R (t?crossprod): methods for pMatrix
485    
486    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
487    
488            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
489    
490    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
491    
492            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
493              trying to fix a subtle bug - which has been somewhere else.
494    
495    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
496    
497            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
498              solve the bug
499    
500    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * src/dgCMatrix.c (compressed_to_TMatrix):
503    
504    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * src/Csparse.c (Rsparse_validate): new, to have some validity
507            checking for RsparseMatrix
508            * src/dgCMatrix.c (xRMatrix_validate): ditto
509            * src/dtCMatrix.c (tRMatrix_validate): ditto
510    
511    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
512    
513          * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in          * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
514            lgRMatrix            lgRMatrix

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