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revision 1847, Sat May 19 19:23:28 2007 UTC revision 2199, Mon Jun 2 16:09:12 2008 UTC
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1    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
4    
5            * R/not.R: fix !<ldiMatrix>
6            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
7    
8            * R/diagMatrix.R (Ops): fix one-off thinko in
9            <diagonal> o <numeric> methods
10    
11            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
12    
13    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
16            * tests/Simple.R: testing the above
17    
18    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
21    
22    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
25            * NAMESPACE (unname): finally exported
26    
27    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/Auxiliaries.R (cholMat): possibly keep packed
30    
31            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
32            for R < 2.7.0.
33    
34            * R/Tsparse.R ([): for triangularMatrix, check if result may be
35            triangular.
36            * tests/indexing.R: regression test
37    
38    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
41            * R/Ops.R: more methods, for lMatrix/nMatrix
42    
43    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/expm.R: new file for all expm() methods; notably new ones for
46            diagonal*, triangular*, symmetric* and also simple "matrix".
47    
48    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
51    
52            * inst/test-tools.R (assert.EQ.mat): better message when not equal
53    
54            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
55    
56            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
57            [dl]denseMatrix {identical slots; but more logical method dispatch}
58    
59    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
62    
63            * R/diagMatrix.R (determinant): method
64    
65    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
68    
69            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
70    
71            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
72            its diagonal
73    
74    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
77    
78            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
79    
80            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
81    
82            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
83    
84    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
87    
88            * R/Ops.R (.do.Logic.lsparse): fix NA case
89    
90            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
91    
92            * R/Auxiliaries.R (nnzero): fix special cases, using
93            * R/Auxiliaries.R (indDiag): new utility
94            * R/Auxiliaries.R (indTri): new argument 'diag'
95    
96            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
97    
98    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
101    
102            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
103            ".tCMatrix" triangular matrix.
104    
105            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
106            'clx' can be class *or* class representation.
107            (nnzSparse): new.
108            (non0ind): new 'xtendSymm' argument; used in
109            * R/Ops.R:
110    
111            * R/pMatrix.R: more efficient determinant() method
112    
113    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
116            * [disactivated] NAMESPACE: export(det)
117    
118            * R/diagMatrix.R (mkDiag): new substitute for diag()
119    
120            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
121            (as0, as1): new utility.
122    
123            * R/Csparse.R (diag, band): need diagU2N()
124    
125            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
126    
127            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
128    
129            * R/Ops.R (Compare): fix <nsp> o <nsp> case
130    
131            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
132    
133    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/Auxiliaries.R (signPerm): new utility for
136            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
137    
138            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
139            since we have our own error handler (and can use tryCatch() from R).
140    
141    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
144    
145            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
146            when not positive definite.
147    
148            * R/Auxiliaries.R (asTri): new auxiliary
149            (non0.i): make *much* faster for Tsparse with many non-zero
150            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
151    
152            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
153            test-tools.R , see below
154    
155            * R/dMatrix.R: fix "Summary" method: + diagU2N()
156    
157            * NAMESPACE, R/Matrix.R: add mean() method
158    
159    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
162            cold-hot colors; try *changed* default useAbs = FALSE
163            * man/image-methods.Rd:  nice examples
164    
165    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * inst/test-tools.R (checkMatrix): new function for modularizing part
168            of tstMatrixClass() in tests/Class+Meth.R
169    
170            * R/dsCMatrix.R: coercion from "matrix"
171            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
172    
173            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
174            add test for as(matrix(,0,0), <class>)
175    
176    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
179            work as determinant(matrix(,0,0)).
180    
181            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
182            * man/sparseLU-class.Rd: ditto
183    
184            * R/dgCMatrix.R (determinant): method building on lu()
185            * R/sparseMatrix.R, Matrix.R, ...: ditto
186    
187            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
188    
189    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
192            pattern matrices.
193    
194    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * src/dense.c (dense_to_Csparse): all declarations *before*
197            R_CheckStack(); needed e.g. for ancient gcc 2.96.
198    
199    
200    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * DESCRIPTION (Version): 0.999375-9 --- need to release
203            for R-devel (and R 2.7.0 alpha soon).
204    
205            * R/AllClass.R: drop "double" from "atomicVector" class union
206    
207            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
208            * R/dgeMatrix.R: ditto
209    
210            * R/sparseMatrix.R (summary): count NAs
211    
212            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
213    
214    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
217            order to become compatible to new R 2.7.0 base::rcond().
218    
219    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
222    
223            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
224    
225            * inst/test-tools.R (isValid): new utility, used much in
226            * tests/simple.R:
227    
228            * man/BunchKaufman-methods.Rd: added too
229    
230    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/dsyMatrix.R: add BunchKaufman() methods.
233            * R/dspMatrix.R:
234    
235            * src/init.c: add dsyMatrix_trf
236    
237    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
238    
239            * DESCRIPTION (Version): release 0.999375-7
240            * src/CHMfactor.c (CHMfactor_update): fix
241    
242    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
245            internal_chm_factor().
246    
247            * R/AllGeneric.R: do *not* define a "chol" generic
248                    (but rather use the implicit one *without* making pivot
249                    part of the signature)
250            * R/*.R: drop the 'pivot' from chol's signature and make
251                    'pivot=FALSE' a default argument of method definitions.
252    
253            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
254            version of Matrix
255    
256    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
259    
260            * R/sparseMatrix.R (is.na): new simple method
261            * R/denseMatrix.R (is.na): ditto.
262    
263            * R/diagMatrix.R (.symDiagonal): newly exported utility.
264    
265            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
266    
267            * src/UFsparse_download.sh: -->
268            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
269    
270    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
273            functionality; barely tested in
274            * tests/factorizing.R
275    
276            * src/Csparse.c (diag_tC): new functionality to enable faster
277            determinant(<dsCMatrix>, .) in
278            * R/dsCMatrix.R
279    
280    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
281    
282            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
283              src/CHMfactor.c, src/CHMfactor.h,
284              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
285              Log-determinant of the parent matrix from a CHMfactor object as
286              chm_factor_ldetL2; documentation and support
287    
288    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
291    
292    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
295            warning.
296    
297    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
300    
301            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
302              <diagonal> o <sparse_triangular>
303              setAs(., "nMatrix") added.
304    
305            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
306    
307            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
308                    new argument 'checkDense = FALSE'.
309    
310    
311    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
314            back-permutation of the matrix exponential.
315    
316            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
317    
318            * DESCRIPTION (Date,Version): ready to release 0.999375-5
319    
320            * tests/simple.R: testing diagN2U
321    
322    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/Auxiliaries.R (diagN2U): interface to
325    
326            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
327    
328            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
329    
330    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * src/chm_common.c (chm_diagN2U): new utility.
333    
334            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
335            make use of chm_diagN2U() and hence now preserve triangularity and
336            unit-triangularity.
337    
338            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
339    
340    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
343    
344            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
345            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
346    
347            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
348    
349            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
350    
351            * src/chm_common.c (AS_CHM_FINISH): add note about problem
352            for triangular (diag = "U").
353    
354    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
357            * R/bind.R:  .Call(dense_to_Csparse, *)
358    
359    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/Matrix.R (Matrix): no longer use coercions to specific classes
362                    (since we are discouraging them in user code).
363    
364            * tests/*.R: also replaces coercions to specific classes by
365            coercions to super classes.
366    
367            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
368    
369    
370    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
373    
374            * src/dense.c (dense_band): generalized from ddense_band
375    
376            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
377              now for "denseMatrix" (instead of just "ddense*"); much
378              simplified setMethod()s for these.
379    
380            * src/dense.c (dense_to_symmetric): generalized from ddense_*
381    
382    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
385            version of as(*, "symmetricMatric").
386    
387            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
388            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
389    
390    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * R/Matrix.R (subset.ij): utility, as first step to faster
393               M [ <ij-matrix> ] indexing.
394    
395            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
396    
397            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
398            for more efficient symmpart() and skewpart() methods.
399    
400            * src/Mutils.c (equal_string_vectors): utility
401    
402            * src/dense.c (ddense_to_symmetric): new function used in
403    
404            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
405    
406            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
407            order to match the generic (and evade .local(..)).
408    
409            * R/dsCMatrix.R: dgC -> dsC: use C code!
410    
411            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
412            as per TODO
413    
414            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
415    
416            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
417    
418    
419    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
422    
423            * R/Auxiliaries.R (non0.i): take out of non0ind
424    
425            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
426            make tril(), triu(), band() work for "matrix" and all "dense*"
427    
428            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
429            * tests/simple.R: test the fix above
430    
431            * R/sparseMatrix.R ([): simplification: no coerce to <general>
432                    before we use as(., <Tsparse>)[...] anyway
433    
434            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
435    
436            * R/triangularMatrix.R (isTriangular): methods for all subclasses
437            instead of "triangularMatrix" -- just to disambiguate
438    
439    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
442            * tests/indexing.R: example that fails above
443    
444    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
447            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
448                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
449    
450            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
451            * src/Tsparse.h, init.c: ditto
452            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
453                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
454            * R/sparseMatrix.R (isTriangular): hence simplified
455    
456    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * R/Ops.R (.Arith.Csparse): new utility factored out of former
459              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
460    
461    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
464    
465            * inst/test-tools.R (isOrthogonal): new function; also file restructured
466    
467    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
470            coercion to "nMatrix" and "pMatrix"
471    
472            * R/AllClass.R: "Schur" class;  "number" class union
473            * man/number-class.Rd:
474            * man/Schur-class.Rd:
475    
476            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
477            (.simpleSchur): Schur() method for diagonal matrices
478            (.triSchur):    Schur() method for triangular matrices
479            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
480    
481    
482    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
485    
486    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
489                    in order to ensure 'system = *' is not lost;
490                    formals()$system instead of cut&paste.
491            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
492    
493    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
494    
495            * DESCRIPTION (Date): make ready for release --> 0.999375-4
496    
497            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
498    
499    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
502                    and hence does as.vector(.).
503            * man/pMatrix-class.Rd: docs
504            * R/sparseMatrix.R: fix for printing "integer sparse"
505    
506            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
507    
508            * R/Matrix.R and others: use "exact" function argument list for
509                    both "["   : (x, i,j, ..., drop)
510                    and  "[<-" : (x, i,j, ..., value)
511    
512            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
513            * R/Tsparse.R (replTmat):    ditto
514            * R/diagMatrix.R (replDiag): ditto
515            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
516            * tests/indexing.R: testing the above
517    
518    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/sparseMatrix.R (cov2cor): method for sparse matrices
521    
522            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
523    
524            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
525    
526            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
527    
528    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
529    
530            * R/Matrix.R: "generic" cov2cor() method
531    
532            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
533                    speed up Q %*% D %*% t(Q)
534            * tests/dpoMatrix.R: test nearPD()
535    
536    2007-12-05  Doug Bates and Martin Maechler
537    
538            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
539            stats::xtabs() allowing to create sparse matrices.
540    
541    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
542    
543            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
544    
545    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
546    
547            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
548    
549    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * R/LU.R: solve() method for "denseLU"
552    
553    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
554    
555            * DESCRIPTION (Version): 0.999375-3 preparing for release
556    
557            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
558    
559            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
560    
561    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
564              thanks to Kasper Kristensen.
565            * tests/matprod.R: regression test for that.
566    
567    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
568    
569            * [r4778] R/AllGeneric.R: Check R version before defining generics for
570              primitives
571    
572    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * R/denseMatrix.R (rcond): method
575            * R/sparseQR.R (rcond): method, use x or t(x)
576    
577    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
580            matrices.
581            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
582    
583            * man/rcond.Rd: mention the more general definition, and add
584            example for non-square matrices.
585    
586            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
587    
588    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
589    
590            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
591    
592    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
595            * tests/indexing.R: add new regression for the above cases.
596    
597    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * src/Mutils.h (__sun): clause for alloca.h on Solaris
600    
601    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * DESCRIPTION (Date, Version): 0.999375-2
604    
605    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * R/HBMM.R (readMM): make work for pattern matrices as well
608    
609    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
610    
611            * [r4730] src/Mutils.h: declare alloca
612            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
613              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
614              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
615              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
616              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
617              methods; switch writeMM to use CHOLMOD code; repair readMM
618    
619    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
622            Oehlschlaegel's ... result type still to be discussed!
623    
624    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * man/image-methods.Rd: new, combining all image() methods
627    
628    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
629    
630            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
631            to work via dgC...
632    
633            * R/Matrix.R (Matrix): special treatment for "table" (S3)
634    
635    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
636    
637            * R/dgTMatrix.R (image): change defaults to
638                    aspect = "iso", colorkey = FALSE
639    
640    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
643            must copy its *expanded* x slot before LAPACK call.
644    
645            * tests/matprod.R: test the last days' changes.
646    
647    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
648    
649            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
650              as well as in sources
651            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
652              Lapack call
653    
654    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
655    
656            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
657                    ("Matrix", "matrix") which is needed in some cases.
658            Ditto for solve().
659    
660            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
661            infinite recursion in dispatch for some cases.
662    
663    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
664    
665            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
666              so pointers match
667    
668    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
669    
670            * DESCRIPTION (Date): set ready for release -- 0.999375-1
671    
672    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
673    
674            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
675              src/chm_common.c, src/chm_common.h: Change API for
676              numeric_as_chm_dense and N_AS_CHM_DN
677    
678    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
681            * tests/matprod.R: regr.test for it
682    
683    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
686            * tests/group-methods.R: and regression-test it
687    
688    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
689    
690            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
691              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
692              triplet_to_sparse, documentation, use typedefs
693    
694    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
695    
696            * man/dpoMatrix-class.Rd: added 'corMatrix' example
697    
698            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
699            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
700            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
701    
702            * R/lsparseMatrix.R: bug fix in "all" method
703            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
704    
705            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
706            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
707                    + matrix |-> nMatrix coercion
708            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
709            * man/pMatrix-class.Rd: ditto
710    
711            * R/Matrix.R (Summary): method for non-dMatrix
712    
713            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
714            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
715                    test all Summary methods.
716    
717    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
718    
719            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
720    
721    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
722    
723            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
724    
725            * R/pMatrix.R (t?crossprod): methods for pMatrix
726    
727    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
728    
729            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
730    
731    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
732    
733            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
734              trying to fix a subtle bug - which has been somewhere else.
735    
736    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
737    
738            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
739              solve the bug
740    
741    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * src/dgCMatrix.c (compressed_to_TMatrix):
744    
745    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * src/Csparse.c (Rsparse_validate): new, to have some validity
748            checking for RsparseMatrix
749            * src/dgCMatrix.c (xRMatrix_validate): ditto
750            * src/dtCMatrix.c (tRMatrix_validate): ditto
751    
752    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
753    
754            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
755              lgRMatrix
756            * [r4568] DESCRIPTION: Prepare for bug-fix release
757            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
758              for declaration of cholmod_symmetry
759    
760    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
761    
762            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
763            release.
764    
765    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
766    
767            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
768              functions - no longer used
769            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
770              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
771              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
772              Alloca
773    
774    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
775    
776            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
777              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
778              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
779              src/t_gCMatrix_colSums.c: more R_CheckStack()s
780    
781    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
782    
783            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
784              the required amount of memory then call M_numeric_as_chm_dense.
785            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
786              (like Calloc but calling alloca)
787    
788    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
789    
790            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
791            and extended with more sophisticated 'col.names' option.
792            * NAMESPACE: export  printSparseMatrix()
793            * man/printSpMatrix.Rd: document, incl. examples
794    
795    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
796    
797            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
798              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
799              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
800    
801    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
802    
803            * DESCRIPTION (Version): 0.99875-4
804    
805            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
806            some dimnames perservation.
807    
808            * R/dsTMatrix.R (t-method): keep dimnames
809            * R/dtTMatrix.R:  ditto
810    
811            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
812            and ncol(.) < 10
813    
814            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
815            from Mutils.h
816    
817            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
818            e.g. in as(<ngCMatrix>, "matrix")
819    
820    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
821    
822            * [r4529] .: Create a branch for the API changes from the 0.99875
823              series to the 0.999375 series
824            * [r4530] DESCRIPTION, inst/include/Matrix.h,
825              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
826              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
827              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
828              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
829              as_cholmod_x functions
830    
831    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
832    
833            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
834              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
835              to Comparisons
836    
837    >>>>>>> .merge-right.r4561
838    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
839    
840            * DESCRIPTION (Version): 0.99875-3 ready to be released.
841    
842            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
843    
844            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
845            that should also work in a future version of R.
846    
847    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
848    
849            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
850    
851            * R/sparseVector.R: more *sparseVector coercions, notably for
852            non - double ones.
853    
854    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
855    
856            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
857              notably the new ones building on the new .Call(.)s:
858    
859            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
860            all 4 of [dlin]gCMatrix_colSums().
861    
862    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
863    
864            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
865            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
866              result
867    
868    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
869    
870            * R/kronecker.R: fix typo (could lead to inf.recursion)
871            * test/simple.R: testing that
872    
873            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
874            method as well (which can have arguments, show() can't).
875    
876    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
877    
878            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
879              added dgCMatrix_colSums for [col,row][Sums,Means]
880    
881    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
882    
883            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
884              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
885              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
886            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
887              class
888            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
889              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
890              row names to store the levels - duh!  Added an example.
891    
892    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
893    
894            * src/Csparse.c (Csparse_validate): check for *repeated* entries
895            thanks to example from Christian Buchta; with a test here:
896            * tests/simple.R:
897    
898    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
899    
900            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
901            of colSums(*, sparseResult = TRUE)
902    
903    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
904    
905            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
906            'na.rm = FALSE' as "everywhere" else in R.
907    
908    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
909    
910            * [r4421] src/CSparse_install.sh: Modify for new organization of
911              CSparse package
912            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
913              SuiteSparse
914            * [r4426] src/Makefile: add ./UFconfig to the include path for
915              compilation
916            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
917            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
918              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
919    
920    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
921    
922            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
923            * R/sparseMatrix.R (prSpMatrix): now gives a message about
924            suppressed column names.
925    
926    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
927    
928            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
929              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
930              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
931              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
932              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
933              Remove warnings after change to const char* CHAR
934    
935    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
936    
937            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
938              type of M_cholmod_ssmult
939    
940    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
941    
942            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
943              src/init.c: Yet another cholmod export - cholmod_ssmult
944    
945    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
946    
947            * NAMESPACE: exported drop0(), since
948            * man/drop0.Rd: I have seen several cases, I really wanted to use
949            it, so our users may want too.
950    
951    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
952    
953            * man/colSums.Rd: separately document colSums() etc, since these
954            have the extra argument 'sparseResult'.
955    
956    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
957    
958            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
959            * man/spMatrix.Rd: docu., including examples
960    
961            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
962            in order to make colMeans() etc fast *and* correct.
963            * R/sparseVector.R (replSPvec): "[<-" functionality for
964            sparseVectors; tested in
965            * tests/simple.R:
966    
967    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
968    
969            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
970            (very) sparse Matrices; output similar to Matlab's print().
971    
972  2007-05-17  Douglas Bates  <bates@stat.wisc.edu>  2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
973    
974          * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not          * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not

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