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revision 1682, Fri Dec 1 18:42:40 2006 UTC revision 2175, Wed Apr 23 11:23:50 2008 UTC
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1    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
4    
5            * R/diagMatrix.R (determinant): method
6    
7    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
10    
11            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
12    
13            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
14            its diagonal
15    
16    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
19    
20            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
21    
22            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
23    
24            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
25    
26    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
29    
30            * R/Ops.R (.do.Logic.lsparse): fix NA case
31    
32            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
33    
34            * R/Auxiliaries.R (nnzero): fix special cases, using
35            * R/Auxiliaries.R (indDiag): new utility
36            * R/Auxiliaries.R (indTri): new argument 'diag'
37    
38            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
39    
40    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
43    
44            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
45            ".tCMatrix" triangular matrix.
46    
47            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
48            'clx' can be class *or* class representation.
49            (nnzSparse): new.
50            (non0ind): new 'xtendSymm' argument; used in
51            * R/Ops.R:
52    
53            * R/pMatrix.R: more efficient determinant() method
54    
55    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
58            * [disactivated] NAMESPACE: export(det)
59    
60            * R/diagMatrix.R (mkDiag): new substitute for diag()
61    
62            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
63            (as0, as1): new utility.
64    
65            * R/Csparse.R (diag, band): need diagU2N()
66    
67            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
68    
69            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
70    
71            * R/Ops.R (Compare): fix <nsp> o <nsp> case
72    
73            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
74    
75    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/Auxiliaries.R (signPerm): new utility for
78            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
79    
80            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
81            since we have our own error handler (and can use tryCatch() from R).
82    
83    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
86    
87            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
88            when not positive definite.
89    
90            * R/Auxiliaries.R (asTri): new auxiliary
91            (non0.i): make *much* faster for Tsparse with many non-zero
92            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
93    
94            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
95            test-tools.R , see below
96    
97            * R/dMatrix.R: fix "Summary" method: + diagU2N()
98    
99            * NAMESPACE, R/Matrix.R: add mean() method
100    
101    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
104            cold-hot colors; try *changed* default useAbs = FALSE
105            * man/image-methods.Rd:  nice examples
106    
107    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * inst/test-tools.R (checkMatrix): new function for modularizing part
110            of tstMatrixClass() in tests/Class+Meth.R
111    
112            * R/dsCMatrix.R: coercion from "matrix"
113            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
114    
115            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
116            add test for as(matrix(,0,0), <class>)
117    
118    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
121            work as determinant(matrix(,0,0)).
122    
123            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
124            * man/sparseLU-class.Rd: ditto
125    
126            * R/dgCMatrix.R (determinant): method building on lu()
127            * R/sparseMatrix.R, Matrix.R, ...: ditto
128    
129            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
130    
131    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
134            pattern matrices.
135    
136    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * src/dense.c (dense_to_Csparse): all declarations *before*
139            R_CheckStack(); needed e.g. for ancient gcc 2.96.
140    
141    
142    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * DESCRIPTION (Version): 0.999375-9 --- need to release
145            for R-devel (and R 2.7.0 alpha soon).
146    
147            * R/AllClass.R: drop "double" from "atomicVector" class union
148    
149            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
150            * R/dgeMatrix.R: ditto
151    
152            * R/sparseMatrix.R (summary): count NAs
153    
154            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
155    
156    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
159            order to become compatible to new R 2.7.0 base::rcond().
160    
161    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
164    
165            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
166    
167            * inst/test-tools.R (isValid): new utility, used much in
168            * tests/simple.R:
169    
170            * man/BunchKaufman-methods.Rd: added too
171    
172    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/dsyMatrix.R: add BunchKaufman() methods.
175            * R/dspMatrix.R:
176    
177            * src/init.c: add dsyMatrix_trf
178    
179    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
180    
181            * DESCRIPTION (Version): release 0.999375-7
182            * src/CHMfactor.c (CHMfactor_update): fix
183    
184    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
187            internal_chm_factor().
188    
189            * R/AllGeneric.R: do *not* define a "chol" generic
190                    (but rather use the implicit one *without* making pivot
191                    part of the signature)
192            * R/*.R: drop the 'pivot' from chol's signature and make
193                    'pivot=FALSE' a default argument of method definitions.
194    
195            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
196            version of Matrix
197    
198    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
201    
202            * R/sparseMatrix.R (is.na): new simple method
203            * R/denseMatrix.R (is.na): ditto.
204    
205            * R/diagMatrix.R (.symDiagonal): newly exported utility.
206    
207            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
208    
209            * src/UFsparse_download.sh: -->
210            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
211    
212    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
215            functionality; barely tested in
216            * tests/factorizing.R
217    
218            * src/Csparse.c (diag_tC): new functionality to enable faster
219            determinant(<dsCMatrix>, .) in
220            * R/dsCMatrix.R
221    
222    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
223    
224            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
225              src/CHMfactor.c, src/CHMfactor.h,
226              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
227              Log-determinant of the parent matrix from a CHMfactor object as
228              chm_factor_ldetL2; documentation and support
229    
230    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
233    
234    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
237            warning.
238    
239    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
242    
243            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
244              <diagonal> o <sparse_triangular>
245              setAs(., "nMatrix") added.
246    
247            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
248    
249            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
250                    new argument 'checkDense = FALSE'.
251    
252    
253    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
256            back-permutation of the matrix exponential.
257    
258            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
259    
260            * DESCRIPTION (Date,Version): ready to release 0.999375-5
261    
262            * tests/simple.R: testing diagN2U
263    
264    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/Auxiliaries.R (diagN2U): interface to
267    
268            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
269    
270            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
271    
272    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * src/chm_common.c (chm_diagN2U): new utility.
275    
276            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
277            make use of chm_diagN2U() and hence now preserve triangularity and
278            unit-triangularity.
279    
280            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
281    
282    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
285    
286            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
287            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
288    
289            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
290    
291            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
292    
293            * src/chm_common.c (AS_CHM_FINISH): add note about problem
294            for triangular (diag = "U").
295    
296    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
299            * R/bind.R:  .Call(dense_to_Csparse, *)
300    
301    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * R/Matrix.R (Matrix): no longer use coercions to specific classes
304                    (since we are discouraging them in user code).
305    
306            * tests/*.R: also replaces coercions to specific classes by
307            coercions to super classes.
308    
309            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
310    
311    
312    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
315    
316            * src/dense.c (dense_band): generalized from ddense_band
317    
318            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
319              now for "denseMatrix" (instead of just "ddense*"); much
320              simplified setMethod()s for these.
321    
322            * src/dense.c (dense_to_symmetric): generalized from ddense_*
323    
324    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
327            version of as(*, "symmetricMatric").
328    
329            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
330            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
331    
332    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/Matrix.R (subset.ij): utility, as first step to faster
335               M [ <ij-matrix> ] indexing.
336    
337            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
338    
339            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
340            for more efficient symmpart() and skewpart() methods.
341    
342            * src/Mutils.c (equal_string_vectors): utility
343    
344            * src/dense.c (ddense_to_symmetric): new function used in
345    
346            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
347    
348            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
349            order to match the generic (and evade .local(..)).
350    
351            * R/dsCMatrix.R: dgC -> dsC: use C code!
352    
353            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
354            as per TODO
355    
356            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
357    
358            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
359    
360    
361    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
364    
365            * R/Auxiliaries.R (non0.i): take out of non0ind
366    
367            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
368            make tril(), triu(), band() work for "matrix" and all "dense*"
369    
370            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
371            * tests/simple.R: test the fix above
372    
373            * R/sparseMatrix.R ([): simplification: no coerce to <general>
374                    before we use as(., <Tsparse>)[...] anyway
375    
376            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
377    
378            * R/triangularMatrix.R (isTriangular): methods for all subclasses
379            instead of "triangularMatrix" -- just to disambiguate
380    
381    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
384            * tests/indexing.R: example that fails above
385    
386    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
389            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
390                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
391    
392            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
393            * src/Tsparse.h, init.c: ditto
394            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
395                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
396            * R/sparseMatrix.R (isTriangular): hence simplified
397    
398    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/Ops.R (.Arith.Csparse): new utility factored out of former
401              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
402    
403    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
406    
407            * inst/test-tools.R (isOrthogonal): new function; also file restructured
408    
409    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
412            coercion to "nMatrix" and "pMatrix"
413    
414            * R/AllClass.R: "Schur" class;  "number" class union
415            * man/number-class.Rd:
416            * man/Schur-class.Rd:
417    
418            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
419            (.simpleSchur): Schur() method for diagonal matrices
420            (.triSchur):    Schur() method for triangular matrices
421            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
422    
423    
424    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
427    
428    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
431                    in order to ensure 'system = *' is not lost;
432                    formals()$system instead of cut&paste.
433            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
434    
435    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * DESCRIPTION (Date): make ready for release --> 0.999375-4
438    
439            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
440    
441    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
444                    and hence does as.vector(.).
445            * man/pMatrix-class.Rd: docs
446            * R/sparseMatrix.R: fix for printing "integer sparse"
447    
448            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
449    
450            * R/Matrix.R and others: use "exact" function argument list for
451                    both "["   : (x, i,j, ..., drop)
452                    and  "[<-" : (x, i,j, ..., value)
453    
454            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
455            * R/Tsparse.R (replTmat):    ditto
456            * R/diagMatrix.R (replDiag): ditto
457            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
458            * tests/indexing.R: testing the above
459    
460    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * R/sparseMatrix.R (cov2cor): method for sparse matrices
463    
464            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
465    
466            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
467    
468            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
469    
470    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * R/Matrix.R: "generic" cov2cor() method
473    
474            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
475                    speed up Q %*% D %*% t(Q)
476            * tests/dpoMatrix.R: test nearPD()
477    
478    2007-12-05  Doug Bates and Martin Maechler
479    
480            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
481            stats::xtabs() allowing to create sparse matrices.
482    
483    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
484    
485            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
486    
487    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
488    
489            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
490    
491    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * R/LU.R: solve() method for "denseLU"
494    
495    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
496    
497            * DESCRIPTION (Version): 0.999375-3 preparing for release
498    
499            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
500    
501            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
502    
503    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
506              thanks to Kasper Kristensen.
507            * tests/matprod.R: regression test for that.
508    
509    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
510    
511            * [r4778] R/AllGeneric.R: Check R version before defining generics for
512              primitives
513    
514    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * R/denseMatrix.R (rcond): method
517            * R/sparseQR.R (rcond): method, use x or t(x)
518    
519    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
522            matrices.
523            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
524    
525            * man/rcond.Rd: mention the more general definition, and add
526            example for non-square matrices.
527    
528            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
529    
530    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
531    
532            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
533    
534    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
535    
536            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
537            * tests/indexing.R: add new regression for the above cases.
538    
539    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * src/Mutils.h (__sun): clause for alloca.h on Solaris
542    
543    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * DESCRIPTION (Date, Version): 0.999375-2
546    
547    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * R/HBMM.R (readMM): make work for pattern matrices as well
550    
551    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
552    
553            * [r4730] src/Mutils.h: declare alloca
554            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
555              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
556              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
557              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
558              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
559              methods; switch writeMM to use CHOLMOD code; repair readMM
560    
561    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
564            Oehlschlaegel's ... result type still to be discussed!
565    
566    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * man/image-methods.Rd: new, combining all image() methods
569    
570    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
571    
572            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
573            to work via dgC...
574    
575            * R/Matrix.R (Matrix): special treatment for "table" (S3)
576    
577    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * R/dgTMatrix.R (image): change defaults to
580                    aspect = "iso", colorkey = FALSE
581    
582    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
585            must copy its *expanded* x slot before LAPACK call.
586    
587            * tests/matprod.R: test the last days' changes.
588    
589    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
590    
591            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
592              as well as in sources
593            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
594              Lapack call
595    
596    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
599                    ("Matrix", "matrix") which is needed in some cases.
600            Ditto for solve().
601    
602            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
603            infinite recursion in dispatch for some cases.
604    
605    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
606    
607            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
608              so pointers match
609    
610    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * DESCRIPTION (Date): set ready for release -- 0.999375-1
613    
614    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
615    
616            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
617              src/chm_common.c, src/chm_common.h: Change API for
618              numeric_as_chm_dense and N_AS_CHM_DN
619    
620    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
621    
622            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
623            * tests/matprod.R: regr.test for it
624    
625    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
626    
627            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
628            * tests/group-methods.R: and regression-test it
629    
630    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
631    
632            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
633              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
634              triplet_to_sparse, documentation, use typedefs
635    
636    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * man/dpoMatrix-class.Rd: added 'corMatrix' example
639    
640            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
641            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
642            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
643    
644            * R/lsparseMatrix.R: bug fix in "all" method
645            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
646    
647            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
648            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
649                    + matrix |-> nMatrix coercion
650            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
651            * man/pMatrix-class.Rd: ditto
652    
653            * R/Matrix.R (Summary): method for non-dMatrix
654    
655            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
656            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
657                    test all Summary methods.
658    
659    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
660    
661            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
662    
663    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
666    
667            * R/pMatrix.R (t?crossprod): methods for pMatrix
668    
669    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
670    
671            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
672    
673    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
674    
675            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
676              trying to fix a subtle bug - which has been somewhere else.
677    
678    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
679    
680            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
681              solve the bug
682    
683    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * src/dgCMatrix.c (compressed_to_TMatrix):
686    
687    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * src/Csparse.c (Rsparse_validate): new, to have some validity
690            checking for RsparseMatrix
691            * src/dgCMatrix.c (xRMatrix_validate): ditto
692            * src/dtCMatrix.c (tRMatrix_validate): ditto
693    
694    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
695    
696            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
697              lgRMatrix
698            * [r4568] DESCRIPTION: Prepare for bug-fix release
699            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
700              for declaration of cholmod_symmetry
701    
702    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
705            release.
706    
707    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
708    
709            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
710              functions - no longer used
711            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
712              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
713              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
714              Alloca
715    
716    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
717    
718            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
719              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
720              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
721              src/t_gCMatrix_colSums.c: more R_CheckStack()s
722    
723    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
724    
725            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
726              the required amount of memory then call M_numeric_as_chm_dense.
727            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
728              (like Calloc but calling alloca)
729    
730    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
731    
732            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
733            and extended with more sophisticated 'col.names' option.
734            * NAMESPACE: export  printSparseMatrix()
735            * man/printSpMatrix.Rd: document, incl. examples
736    
737    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
738    
739            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
740              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
741              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
742    
743    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
744    
745            * DESCRIPTION (Version): 0.99875-4
746    
747            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
748            some dimnames perservation.
749    
750            * R/dsTMatrix.R (t-method): keep dimnames
751            * R/dtTMatrix.R:  ditto
752    
753            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
754            and ncol(.) < 10
755    
756            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
757            from Mutils.h
758    
759            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
760            e.g. in as(<ngCMatrix>, "matrix")
761    
762    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
763    
764            * [r4529] .: Create a branch for the API changes from the 0.99875
765              series to the 0.999375 series
766            * [r4530] DESCRIPTION, inst/include/Matrix.h,
767              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
768              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
769              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
770              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
771              as_cholmod_x functions
772    
773    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
774    
775            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
776              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
777              to Comparisons
778    
779    >>>>>>> .merge-right.r4561
780    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
781    
782            * DESCRIPTION (Version): 0.99875-3 ready to be released.
783    
784            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
785    
786            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
787            that should also work in a future version of R.
788    
789    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
792    
793            * R/sparseVector.R: more *sparseVector coercions, notably for
794            non - double ones.
795    
796    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
797    
798            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
799              notably the new ones building on the new .Call(.)s:
800    
801            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
802            all 4 of [dlin]gCMatrix_colSums().
803    
804    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
805    
806            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
807            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
808              result
809    
810    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
811    
812            * R/kronecker.R: fix typo (could lead to inf.recursion)
813            * test/simple.R: testing that
814    
815            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
816            method as well (which can have arguments, show() can't).
817    
818    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
819    
820            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
821              added dgCMatrix_colSums for [col,row][Sums,Means]
822    
823    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
824    
825            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
826              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
827              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
828            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
829              class
830            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
831              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
832              row names to store the levels - duh!  Added an example.
833    
834    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
835    
836            * src/Csparse.c (Csparse_validate): check for *repeated* entries
837            thanks to example from Christian Buchta; with a test here:
838            * tests/simple.R:
839    
840    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
841    
842            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
843            of colSums(*, sparseResult = TRUE)
844    
845    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
846    
847            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
848            'na.rm = FALSE' as "everywhere" else in R.
849    
850    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
851    
852            * [r4421] src/CSparse_install.sh: Modify for new organization of
853              CSparse package
854            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
855              SuiteSparse
856            * [r4426] src/Makefile: add ./UFconfig to the include path for
857              compilation
858            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
859            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
860              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
861    
862    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
863    
864            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
865            * R/sparseMatrix.R (prSpMatrix): now gives a message about
866            suppressed column names.
867    
868    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
869    
870            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
871              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
872              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
873              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
874              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
875              Remove warnings after change to const char* CHAR
876    
877    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
878    
879            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
880              type of M_cholmod_ssmult
881    
882    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
883    
884            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
885              src/init.c: Yet another cholmod export - cholmod_ssmult
886    
887    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
888    
889            * NAMESPACE: exported drop0(), since
890            * man/drop0.Rd: I have seen several cases, I really wanted to use
891            it, so our users may want too.
892    
893    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
894    
895            * man/colSums.Rd: separately document colSums() etc, since these
896            have the extra argument 'sparseResult'.
897    
898    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
899    
900            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
901            * man/spMatrix.Rd: docu., including examples
902    
903            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
904            in order to make colMeans() etc fast *and* correct.
905            * R/sparseVector.R (replSPvec): "[<-" functionality for
906            sparseVectors; tested in
907            * tests/simple.R:
908    
909    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
910    
911            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
912            (very) sparse Matrices; output similar to Matlab's print().
913    
914    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
915    
916            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
917            0-based, indices (Jose Quesada <quesada@gmail.com>).
918    
919    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
920    
921            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
922    
923    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
924    
925            * R/Auxiliaries.R (sparsapply): new utility, much faster than
926            tapply1() for large sparse matrices.
927    
928    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
929    
930            * R/Matrix.R (dim<-): reshape now via sparseVector.
931    
932            * R/sparseVector.R: methods and function for
933            * R/AllClass.R: new "sparseVector" class and daughters.
934            * NAMESPACE: export new classes
935    
936    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
937    
938            * DESCRIPTION (Version): 0.99875-1
939            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
940    
941    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
942    
943            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
944            indexing
945            * tests/indexing.R: test set for that.
946    
947    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
948    
949            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
950            entries.
951            * tests/indexing.R(out): add regression test for it
952    
953    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
954    
955            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
956            name for "!" method definitions.
957    
958    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
959    
960            * R/Tsparse.R (intI): new utility, used for "[" :
961                    Cleanup up there, and fixes for duplicated indices - more TODO!
962    
963            * tests/indexing.R(out): more tests
964    
965    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
966    
967            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
968            code that is now part of the R Lapack library.
969    
970            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
971            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
972    
973    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
974    
975            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
976    
977    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
978    
979            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
980            up with extraneous names '0'...'<n-1>'
981    
982    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
983    
984            * R/dgTMatrix.R (mat2dgT): care about NAs
985    
986    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
987    
988            * R/kronecker.R: triangularity preserving methods
989    
990    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
991    
992            * R/kronecker.R: new file collecting kronecker() methods in one
993                    place.  Goal: become much faster!
994    
995    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
998            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
999            can be much faster.
1000    
1001            * tests/matprod.R: add regression tests for these (upper & lower).
1002    
1003    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1004    
1005            * R/Matrix.R (diff): method for our Matrices.
1006    
1007            * R/sparseMatrix.R (isDiagonal): check dim()!
1008    
1009    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1010    
1011            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1012            proposal from Tamas Papp.
1013    
1014    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1015    
1016            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1017    
1018            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1019            rather define and export  cBind() and rBind() only.
1020            --> useRs *must* change code that used to have cbind()/rbind() !!
1021    
1022            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1023            * R/bind.Rout.save: ditto
1024    
1025    2007-02-16  Douglas Bates  <bates@r-project.org>
1026    
1027            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1028            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1029            const modifier on declaration of the array 'valid'
1030    
1031    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1032    
1033            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1034    
1035    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1036    
1037            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1038    
1039            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1040            * tests/simple.R: test the above and some of these coercions:
1041    
1042            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1043                    be careful to avoid infinite recursion, using new coercions in
1044            * R/ngCMatrix.R and nsC... and ntC...
1045            * R/lsparseMatrix.R: ditto
1046    
1047            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1048    
1049            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1050            * R/Rsparse.R: reactivate .Call()s
1051    
1052            * tests/Class+Meth.R: a bit more on actual classes
1053    
1054    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1055    
1056            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1057    
1058    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1059    
1060            * DESCRIPTION (Version): 0.9975-10 to upload
1061    
1062            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1063            specific classes less unconditionally.
1064    
1065            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1066    
1067            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1068    
1069            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1070            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1071            R_to_CMatrix segfaults on one platform.
1072            Eliminate most coercion method to *specific* classes, and replace
1073            with virtual classes coercions.
1074    
1075    
1076    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1077    
1078            * src/init.c: export the CHM...._validate() placeholders, since
1079            they *are* called.
1080    
1081            * tests/Class+Meth.R (classCanCoerce): and starting to test
1082            all as(<from>, <to>)
1083    
1084    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1085    
1086            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1087            * tests/indexing.R: tested now
1088            * tests/indexing.Rout.save: updated
1089    
1090            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1091            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1092            appropriate.
1093    
1094            * NAMESPACE: export a trivial
1095            * R/Matrix.R: drop() Matrix-method
1096    
1097            * R/AllClass.R: moved all prototypes to virtual super classes.
1098    
1099            * R/Rsparse.R: many more coercions to have less exceptions in
1100            * tests/Class+Meth.R:
1101    
1102            * R/Ops.R (Compare): tweak for case with NA
1103            * tests/simpl.R: hence another 'FIXME' eliminated
1104    
1105    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1106    
1107            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1108            objects.
1109    
1110            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1111              and more of "!", "&", "|", all, any; coercions
1112    
1113            * R/Rsparse.R: many coercions (which enable quite a few other
1114            methods), thanks to enhancements in
1115            * src/dgCMatrix.c (R_to_CMatrix): new, and
1116            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1117            symmetric & triangular and ..RMatrix objects.
1118    
1119            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1120            renamed file from src/dsTMatrix.c;
1121            now dealing with symmetric and triangular Tsparse coercions, both
1122            to dense and general.
1123    
1124    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1125    
1126            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1127    
1128            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1129            where sensible when the <numeric> is of length > 1.
1130    
1131    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1132    
1133            * R/Matrix.R ([<-): for M[] <- value: fix length
1134    
1135    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1136    
1137            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1138            * R/ndenseMatrix.R: new coercions n* -> l*
1139    
1140    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1141    
1142            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1143    
1144            * R/Ops.R ("Logic"): and other "Ops", many updates
1145    
1146    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1147    
1148            * src/Mutils.h (SET_DimNames): new utility
1149    
1150            * R/Auxiliaries.R (nnzero): improved and now exported via
1151    
1152            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1153    
1154    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1155    
1156            * R/diagMatrix.R (!): fix typo.
1157    
1158    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1159    
1160            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1161                    allow to pass class definition --> speedup
1162            * R/sparseMatrix.R: apply the above
1163    
1164            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1165    
1166            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1167            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1168            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1169    
1170            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1171    
1172            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1173            and use it for "sparse*" as well, since it's faster than the
1174            as_Csparse(.) way.
1175    
1176    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1177    
1178            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1179    
1180    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1181    
1182            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1183            as method for   M[ ij ] <- v
1184            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1185    
1186            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1187            FALSE answer
1188    
1189            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1190            * tests/indexing.R: test it, and some of the above
1191    
1192    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1193    
1194            * R/Auxiliaries.R (is_duplicatedT): new utility
1195    
1196    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1197    
1198            * src/init.c (R_init_Matrix): export cholmod_scale
1199    
1200    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1201    
1202            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1203            base::as.matrix to (x, ...)
1204    
1205    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1206    
1207            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1208            file; start using "Logic", hence
1209    
1210            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1211            * NAMESPACE: import and export "Logic"
1212    
1213    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1214    
1215            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1216            only needed previously to R version 2.5.0.
1217    
1218    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1219    
1220            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1221    
1222            * R/Tsparse.R (replTmat): fix subassignment of triangular
1223            * R/Csparse.R (replCmat): ditto
1224            * tests/indexing.R: more tests, incl the above fix
1225    
1226    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1227    
1228            * R/Auxiliaries.R (drop0): extend for non CSparse
1229            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1230    
1231            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1232                    use uplo correctly (!); other places: use uplo_P() macro
1233    
1234            * R/Csparse.R (replCmat): call diagU2N() when needed
1235            * R/Tsparse.R (replTmat): ditto
1236    
1237            * src/dtCMatrix.c (tCMatrix_validate): new
1238            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1239            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1240    
1241            * R/diagMatrix.R (replDiag): to use in [<-
1242    
1243    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1244    
1245            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1246                    also more general diagU2N().
1247    
1248    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1249    
1250            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1251            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1252    
1253    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1254    
1255            * tests/bind.R: a few more cases
1256            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1257    
1258            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1259            * R/ddenseMatrix.R (cbind2/rbind2)
1260            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1261            * tests/indexing.R
1262            * tests/indexing.Rout.save: updated
1263    
1264    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1265    
1266            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1267            * tests/indexing.R
1268    
1269    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1270    
1271            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1272            align with proper position of "0", i.e., right for integers.
1273            argument 'align' by default is "fancy".
1274    
1275    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1276    
1277            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1278            * R/Csparse.R: and fix "Compare" for more cases.
1279            * tests/Class+Meth.R: test some of these (m == m, m != m)
1280    
1281    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1282    
1283            * R/lsparseMatrix.R: all() and any() methods
1284            * R/ldenseMatrix.R:      ditto
1285            * NAMESPACE, R/Matrix.R: ditto
1286    
1287            * man/all-methods.Rd: document them minimally
1288    
1289            * tests/simple.R: add a few examples for these
1290    
1291    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1292    
1293            * R/Tsparse.R ([): fix long standing typo in symmetric case
1294            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1295    
1296    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1297    
1298            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1299            to LL before converting to a sparse matrix. (The LDL form can be
1300            converted to a sparse matrix but it is implicitly a unit
1301            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1302    
1303    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1304    
1305            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1306    
1307    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1308    
1309            * DESCRIPTION (Version): updated -> release 0.9975-7
1310            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1311    
1312  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1313    
1314          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method

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