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revision 1852, Mon May 21 16:42:35 2007 UTC revision 2202, Mon Jun 9 21:36:21 2008 UTC
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1    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dtCMatrix.R: faster dgC* -> dtC* method
4            * tests/Simple.R: (hence removed "FIXME")
5    
6            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
7            which can be be turned off for possible speed gains.
8    
9    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
12    
13            * R/not.R: fix !<ldiMatrix>
14            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
15    
16            * R/diagMatrix.R (Ops): fix one-off thinko in
17            <diagonal> o <numeric> methods
18    
19            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
20    
21    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
24            * tests/Simple.R: testing the above
25    
26    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
29    
30    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
33            * NAMESPACE (unname): finally exported
34    
35    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/Auxiliaries.R (cholMat): possibly keep packed
38    
39            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
40            for R < 2.7.0.
41    
42            * R/Tsparse.R ([): for triangularMatrix, check if result may be
43            triangular.
44            * tests/indexing.R: regression test
45    
46    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
49            * R/Ops.R: more methods, for lMatrix/nMatrix
50    
51    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/expm.R: new file for all expm() methods; notably new ones for
54            diagonal*, triangular*, symmetric* and also simple "matrix".
55    
56    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
59    
60            * inst/test-tools.R (assert.EQ.mat): better message when not equal
61    
62            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
63    
64            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
65            [dl]denseMatrix {identical slots; but more logical method dispatch}
66    
67    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
70    
71            * R/diagMatrix.R (determinant): method
72    
73    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
76    
77            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
78    
79            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
80            its diagonal
81    
82    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
85    
86            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
87    
88            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
89    
90            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
91    
92    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
95    
96            * R/Ops.R (.do.Logic.lsparse): fix NA case
97    
98            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
99    
100            * R/Auxiliaries.R (nnzero): fix special cases, using
101            * R/Auxiliaries.R (indDiag): new utility
102            * R/Auxiliaries.R (indTri): new argument 'diag'
103    
104            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
105    
106    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
109    
110            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
111            ".tCMatrix" triangular matrix.
112    
113            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
114            'clx' can be class *or* class representation.
115            (nnzSparse): new.
116            (non0ind): new 'xtendSymm' argument; used in
117            * R/Ops.R:
118    
119            * R/pMatrix.R: more efficient determinant() method
120    
121    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
124            * [disactivated] NAMESPACE: export(det)
125    
126            * R/diagMatrix.R (mkDiag): new substitute for diag()
127    
128            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
129            (as0, as1): new utility.
130    
131            * R/Csparse.R (diag, band): need diagU2N()
132    
133            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
134    
135            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
136    
137            * R/Ops.R (Compare): fix <nsp> o <nsp> case
138    
139            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
140    
141    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/Auxiliaries.R (signPerm): new utility for
144            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
145    
146            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
147            since we have our own error handler (and can use tryCatch() from R).
148    
149    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
152    
153            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
154            when not positive definite.
155    
156            * R/Auxiliaries.R (asTri): new auxiliary
157            (non0.i): make *much* faster for Tsparse with many non-zero
158            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
159    
160            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
161            test-tools.R , see below
162    
163            * R/dMatrix.R: fix "Summary" method: + diagU2N()
164    
165            * NAMESPACE, R/Matrix.R: add mean() method
166    
167    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
170            cold-hot colors; try *changed* default useAbs = FALSE
171            * man/image-methods.Rd:  nice examples
172    
173    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * inst/test-tools.R (checkMatrix): new function for modularizing part
176            of tstMatrixClass() in tests/Class+Meth.R
177    
178            * R/dsCMatrix.R: coercion from "matrix"
179            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
180    
181            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
182            add test for as(matrix(,0,0), <class>)
183    
184    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
187            work as determinant(matrix(,0,0)).
188    
189            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
190            * man/sparseLU-class.Rd: ditto
191    
192            * R/dgCMatrix.R (determinant): method building on lu()
193            * R/sparseMatrix.R, Matrix.R, ...: ditto
194    
195            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
196    
197    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
200            pattern matrices.
201    
202    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * src/dense.c (dense_to_Csparse): all declarations *before*
205            R_CheckStack(); needed e.g. for ancient gcc 2.96.
206    
207    
208    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * DESCRIPTION (Version): 0.999375-9 --- need to release
211            for R-devel (and R 2.7.0 alpha soon).
212    
213            * R/AllClass.R: drop "double" from "atomicVector" class union
214    
215            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
216            * R/dgeMatrix.R: ditto
217    
218            * R/sparseMatrix.R (summary): count NAs
219    
220            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
221    
222    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
225            order to become compatible to new R 2.7.0 base::rcond().
226    
227    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
230    
231            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
232    
233            * inst/test-tools.R (isValid): new utility, used much in
234            * tests/simple.R:
235    
236            * man/BunchKaufman-methods.Rd: added too
237    
238    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/dsyMatrix.R: add BunchKaufman() methods.
241            * R/dspMatrix.R:
242    
243            * src/init.c: add dsyMatrix_trf
244    
245    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
246    
247            * DESCRIPTION (Version): release 0.999375-7
248            * src/CHMfactor.c (CHMfactor_update): fix
249    
250    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
253            internal_chm_factor().
254    
255            * R/AllGeneric.R: do *not* define a "chol" generic
256                    (but rather use the implicit one *without* making pivot
257                    part of the signature)
258            * R/*.R: drop the 'pivot' from chol's signature and make
259                    'pivot=FALSE' a default argument of method definitions.
260    
261            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
262            version of Matrix
263    
264    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
267    
268            * R/sparseMatrix.R (is.na): new simple method
269            * R/denseMatrix.R (is.na): ditto.
270    
271            * R/diagMatrix.R (.symDiagonal): newly exported utility.
272    
273            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
274    
275            * src/UFsparse_download.sh: -->
276            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
277    
278    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
281            functionality; barely tested in
282            * tests/factorizing.R
283    
284            * src/Csparse.c (diag_tC): new functionality to enable faster
285            determinant(<dsCMatrix>, .) in
286            * R/dsCMatrix.R
287    
288    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
289    
290            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
291              src/CHMfactor.c, src/CHMfactor.h,
292              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
293              Log-determinant of the parent matrix from a CHMfactor object as
294              chm_factor_ldetL2; documentation and support
295    
296    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
299    
300    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
303            warning.
304    
305    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
308    
309            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
310              <diagonal> o <sparse_triangular>
311              setAs(., "nMatrix") added.
312    
313            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
314    
315            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
316                    new argument 'checkDense = FALSE'.
317    
318    
319    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
322            back-permutation of the matrix exponential.
323    
324            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
325    
326            * DESCRIPTION (Date,Version): ready to release 0.999375-5
327    
328            * tests/simple.R: testing diagN2U
329    
330    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/Auxiliaries.R (diagN2U): interface to
333    
334            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
335    
336            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
337    
338    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * src/chm_common.c (chm_diagN2U): new utility.
341    
342            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
343            make use of chm_diagN2U() and hence now preserve triangularity and
344            unit-triangularity.
345    
346            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
347    
348    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
351    
352            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
353            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
354    
355            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
356    
357            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
358    
359            * src/chm_common.c (AS_CHM_FINISH): add note about problem
360            for triangular (diag = "U").
361    
362    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
365            * R/bind.R:  .Call(dense_to_Csparse, *)
366    
367    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * R/Matrix.R (Matrix): no longer use coercions to specific classes
370                    (since we are discouraging them in user code).
371    
372            * tests/*.R: also replaces coercions to specific classes by
373            coercions to super classes.
374    
375            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
376    
377    
378    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
381    
382            * src/dense.c (dense_band): generalized from ddense_band
383    
384            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
385              now for "denseMatrix" (instead of just "ddense*"); much
386              simplified setMethod()s for these.
387    
388            * src/dense.c (dense_to_symmetric): generalized from ddense_*
389    
390    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
393            version of as(*, "symmetricMatric").
394    
395            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
396            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
397    
398    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/Matrix.R (subset.ij): utility, as first step to faster
401               M [ <ij-matrix> ] indexing.
402    
403            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
404    
405            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
406            for more efficient symmpart() and skewpart() methods.
407    
408            * src/Mutils.c (equal_string_vectors): utility
409    
410            * src/dense.c (ddense_to_symmetric): new function used in
411    
412            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
413    
414            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
415            order to match the generic (and evade .local(..)).
416    
417            * R/dsCMatrix.R: dgC -> dsC: use C code!
418    
419            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
420            as per TODO
421    
422            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
423    
424            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
425    
426    
427    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
430    
431            * R/Auxiliaries.R (non0.i): take out of non0ind
432    
433            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
434            make tril(), triu(), band() work for "matrix" and all "dense*"
435    
436            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
437            * tests/simple.R: test the fix above
438    
439            * R/sparseMatrix.R ([): simplification: no coerce to <general>
440                    before we use as(., <Tsparse>)[...] anyway
441    
442            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
443    
444            * R/triangularMatrix.R (isTriangular): methods for all subclasses
445            instead of "triangularMatrix" -- just to disambiguate
446    
447    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
450            * tests/indexing.R: example that fails above
451    
452    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
455            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
456                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
457    
458            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
459            * src/Tsparse.h, init.c: ditto
460            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
461                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
462            * R/sparseMatrix.R (isTriangular): hence simplified
463    
464    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * R/Ops.R (.Arith.Csparse): new utility factored out of former
467              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
468    
469    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
472    
473            * inst/test-tools.R (isOrthogonal): new function; also file restructured
474    
475    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
478            coercion to "nMatrix" and "pMatrix"
479    
480            * R/AllClass.R: "Schur" class;  "number" class union
481            * man/number-class.Rd:
482            * man/Schur-class.Rd:
483    
484            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
485            (.simpleSchur): Schur() method for diagonal matrices
486            (.triSchur):    Schur() method for triangular matrices
487            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
488    
489    
490    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
493    
494    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
497                    in order to ensure 'system = *' is not lost;
498                    formals()$system instead of cut&paste.
499            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
500    
501    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
502    
503            * DESCRIPTION (Date): make ready for release --> 0.999375-4
504    
505            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
506    
507    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
508    
509            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
510                    and hence does as.vector(.).
511            * man/pMatrix-class.Rd: docs
512            * R/sparseMatrix.R: fix for printing "integer sparse"
513    
514            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
515    
516            * R/Matrix.R and others: use "exact" function argument list for
517                    both "["   : (x, i,j, ..., drop)
518                    and  "[<-" : (x, i,j, ..., value)
519    
520            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
521            * R/Tsparse.R (replTmat):    ditto
522            * R/diagMatrix.R (replDiag): ditto
523            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
524            * tests/indexing.R: testing the above
525    
526    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
527    
528            * R/sparseMatrix.R (cov2cor): method for sparse matrices
529    
530            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
531    
532            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
533    
534            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
535    
536    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
538            * R/Matrix.R: "generic" cov2cor() method
539    
540            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
541                    speed up Q %*% D %*% t(Q)
542            * tests/dpoMatrix.R: test nearPD()
543    
544    2007-12-05  Doug Bates and Martin Maechler
545    
546            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
547            stats::xtabs() allowing to create sparse matrices.
548    
549    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
552    
553    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
554    
555            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
556    
557    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/LU.R: solve() method for "denseLU"
560    
561    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * DESCRIPTION (Version): 0.999375-3 preparing for release
564    
565            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
566    
567            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
568    
569    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
572              thanks to Kasper Kristensen.
573            * tests/matprod.R: regression test for that.
574    
575    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
576    
577            * [r4778] R/AllGeneric.R: Check R version before defining generics for
578              primitives
579    
580    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * R/denseMatrix.R (rcond): method
583            * R/sparseQR.R (rcond): method, use x or t(x)
584    
585    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
588            matrices.
589            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
590    
591            * man/rcond.Rd: mention the more general definition, and add
592            example for non-square matrices.
593    
594            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
595    
596    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
599    
600    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
601    
602            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
603            * tests/indexing.R: add new regression for the above cases.
604    
605    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * src/Mutils.h (__sun): clause for alloca.h on Solaris
608    
609    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * DESCRIPTION (Date, Version): 0.999375-2
612    
613    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/HBMM.R (readMM): make work for pattern matrices as well
616    
617    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
618    
619            * [r4730] src/Mutils.h: declare alloca
620            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
621              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
622              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
623              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
624              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
625              methods; switch writeMM to use CHOLMOD code; repair readMM
626    
627    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
630            Oehlschlaegel's ... result type still to be discussed!
631    
632    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * man/image-methods.Rd: new, combining all image() methods
635    
636    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
639            to work via dgC...
640    
641            * R/Matrix.R (Matrix): special treatment for "table" (S3)
642    
643    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * R/dgTMatrix.R (image): change defaults to
646                    aspect = "iso", colorkey = FALSE
647    
648    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
649    
650            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
651            must copy its *expanded* x slot before LAPACK call.
652    
653            * tests/matprod.R: test the last days' changes.
654    
655    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
656    
657            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
658              as well as in sources
659            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
660              Lapack call
661    
662    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
665                    ("Matrix", "matrix") which is needed in some cases.
666            Ditto for solve().
667    
668            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
669            infinite recursion in dispatch for some cases.
670    
671    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
672    
673            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
674              so pointers match
675    
676    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * DESCRIPTION (Date): set ready for release -- 0.999375-1
679    
680    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
681    
682            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
683              src/chm_common.c, src/chm_common.h: Change API for
684              numeric_as_chm_dense and N_AS_CHM_DN
685    
686    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
687    
688            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
689            * tests/matprod.R: regr.test for it
690    
691    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
694            * tests/group-methods.R: and regression-test it
695    
696    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
697    
698            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
699              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
700              triplet_to_sparse, documentation, use typedefs
701    
702    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * man/dpoMatrix-class.Rd: added 'corMatrix' example
705    
706            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
707            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
708            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
709    
710            * R/lsparseMatrix.R: bug fix in "all" method
711            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
712    
713            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
714            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
715                    + matrix |-> nMatrix coercion
716            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
717            * man/pMatrix-class.Rd: ditto
718    
719            * R/Matrix.R (Summary): method for non-dMatrix
720    
721            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
722            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
723                    test all Summary methods.
724    
725    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
728    
729    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
732    
733            * R/pMatrix.R (t?crossprod): methods for pMatrix
734    
735    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
736    
737            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
738    
739    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
740    
741            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
742              trying to fix a subtle bug - which has been somewhere else.
743    
744    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
745    
746            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
747              solve the bug
748    
749    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
750    
751            * src/dgCMatrix.c (compressed_to_TMatrix):
752    
753    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * src/Csparse.c (Rsparse_validate): new, to have some validity
756            checking for RsparseMatrix
757            * src/dgCMatrix.c (xRMatrix_validate): ditto
758            * src/dtCMatrix.c (tRMatrix_validate): ditto
759    
760    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
761    
762            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
763              lgRMatrix
764            * [r4568] DESCRIPTION: Prepare for bug-fix release
765            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
766              for declaration of cholmod_symmetry
767    
768    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
769    
770            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
771            release.
772    
773    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
774    
775            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
776              functions - no longer used
777            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
778              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
779              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
780              Alloca
781    
782    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
783    
784            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
785              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
786              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
787              src/t_gCMatrix_colSums.c: more R_CheckStack()s
788    
789    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
790    
791            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
792              the required amount of memory then call M_numeric_as_chm_dense.
793            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
794              (like Calloc but calling alloca)
795    
796    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
797    
798            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
799            and extended with more sophisticated 'col.names' option.
800            * NAMESPACE: export  printSparseMatrix()
801            * man/printSpMatrix.Rd: document, incl. examples
802    
803    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
804    
805            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
806              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
807              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
808    
809    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
810    
811            * DESCRIPTION (Version): 0.99875-4
812    
813            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
814            some dimnames perservation.
815    
816            * R/dsTMatrix.R (t-method): keep dimnames
817            * R/dtTMatrix.R:  ditto
818    
819            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
820            and ncol(.) < 10
821    
822            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
823            from Mutils.h
824    
825            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
826            e.g. in as(<ngCMatrix>, "matrix")
827    
828    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
829    
830            * [r4529] .: Create a branch for the API changes from the 0.99875
831              series to the 0.999375 series
832            * [r4530] DESCRIPTION, inst/include/Matrix.h,
833              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
834              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
835              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
836              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
837              as_cholmod_x functions
838    
839    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
840    
841            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
842              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
843              to Comparisons
844    
845    >>>>>>> .merge-right.r4561
846    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
847    
848            * DESCRIPTION (Version): 0.99875-3 ready to be released.
849    
850            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
851    
852            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
853            that should also work in a future version of R.
854    
855    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
858    
859            * R/sparseVector.R: more *sparseVector coercions, notably for
860            non - double ones.
861    
862    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
863    
864            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
865              notably the new ones building on the new .Call(.)s:
866    
867            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
868            all 4 of [dlin]gCMatrix_colSums().
869    
870    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
871    
872            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
873            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
874              result
875    
876    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
877    
878            * R/kronecker.R: fix typo (could lead to inf.recursion)
879            * test/simple.R: testing that
880    
881            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
882            method as well (which can have arguments, show() can't).
883    
884    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
885    
886            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
887              added dgCMatrix_colSums for [col,row][Sums,Means]
888    
889    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
890    
891            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
892              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
893              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
894            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
895              class
896            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
897              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
898              row names to store the levels - duh!  Added an example.
899    
900    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
901    
902            * src/Csparse.c (Csparse_validate): check for *repeated* entries
903            thanks to example from Christian Buchta; with a test here:
904            * tests/simple.R:
905    
906    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
907    
908            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
909            of colSums(*, sparseResult = TRUE)
910    
911    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
912    
913            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
914            'na.rm = FALSE' as "everywhere" else in R.
915    
916    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
917    
918            * [r4421] src/CSparse_install.sh: Modify for new organization of
919              CSparse package
920            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
921              SuiteSparse
922            * [r4426] src/Makefile: add ./UFconfig to the include path for
923              compilation
924            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
925            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
926              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
927    
928    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
929    
930            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
931            * R/sparseMatrix.R (prSpMatrix): now gives a message about
932            suppressed column names.
933    
934    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
935    
936            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
937              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
938              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
939              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
940              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
941              Remove warnings after change to const char* CHAR
942    
943    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
944    
945            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
946              type of M_cholmod_ssmult
947    
948    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
949    
950            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
951              src/init.c: Yet another cholmod export - cholmod_ssmult
952    
953    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
954    
955            * NAMESPACE: exported drop0(), since
956            * man/drop0.Rd: I have seen several cases, I really wanted to use
957            it, so our users may want too.
958    
959    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
960    
961            * man/colSums.Rd: separately document colSums() etc, since these
962            have the extra argument 'sparseResult'.
963    
964  2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
965    
966          * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;          * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;

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