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revision 1646, Sun Oct 22 22:42:40 2006 UTC revision 2194, Tue May 20 06:44:19 2008 UTC
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1    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
4    
5    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
8            * NAMESPACE (unname): finally exported
9    
10    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/Auxiliaries.R (cholMat): possibly keep packed
13    
14            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
15            for R < 2.7.0.
16    
17            * R/Tsparse.R ([): for triangularMatrix, check if result may be
18            triangular.
19            * tests/indexing.R: regression test
20    
21    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
24            * R/Ops.R: more methods, for lMatrix/nMatrix
25    
26    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/expm.R: new file for all expm() methods; notably new ones for
29            diagonal*, triangular*, symmetric* and also simple "matrix".
30    
31    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
34    
35            * inst/test-tools.R (assert.EQ.mat): better message when not equal
36    
37            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
38    
39            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
40            [dl]denseMatrix {identical slots; but more logical method dispatch}
41    
42    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
45    
46            * R/diagMatrix.R (determinant): method
47    
48    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
51    
52            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
53    
54            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
55            its diagonal
56    
57    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
60    
61            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
62    
63            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
64    
65            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
66    
67    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
70    
71            * R/Ops.R (.do.Logic.lsparse): fix NA case
72    
73            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
74    
75            * R/Auxiliaries.R (nnzero): fix special cases, using
76            * R/Auxiliaries.R (indDiag): new utility
77            * R/Auxiliaries.R (indTri): new argument 'diag'
78    
79            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
80    
81    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
84    
85            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
86            ".tCMatrix" triangular matrix.
87    
88            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
89            'clx' can be class *or* class representation.
90            (nnzSparse): new.
91            (non0ind): new 'xtendSymm' argument; used in
92            * R/Ops.R:
93    
94            * R/pMatrix.R: more efficient determinant() method
95    
96    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
99            * [disactivated] NAMESPACE: export(det)
100    
101            * R/diagMatrix.R (mkDiag): new substitute for diag()
102    
103            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
104            (as0, as1): new utility.
105    
106            * R/Csparse.R (diag, band): need diagU2N()
107    
108            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
109    
110            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
111    
112            * R/Ops.R (Compare): fix <nsp> o <nsp> case
113    
114            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
115    
116    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Auxiliaries.R (signPerm): new utility for
119            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
120    
121            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
122            since we have our own error handler (and can use tryCatch() from R).
123    
124    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
127    
128            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
129            when not positive definite.
130    
131            * R/Auxiliaries.R (asTri): new auxiliary
132            (non0.i): make *much* faster for Tsparse with many non-zero
133            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
134    
135            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
136            test-tools.R , see below
137    
138            * R/dMatrix.R: fix "Summary" method: + diagU2N()
139    
140            * NAMESPACE, R/Matrix.R: add mean() method
141    
142    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
145            cold-hot colors; try *changed* default useAbs = FALSE
146            * man/image-methods.Rd:  nice examples
147    
148    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * inst/test-tools.R (checkMatrix): new function for modularizing part
151            of tstMatrixClass() in tests/Class+Meth.R
152    
153            * R/dsCMatrix.R: coercion from "matrix"
154            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
155    
156            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
157            add test for as(matrix(,0,0), <class>)
158    
159    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
162            work as determinant(matrix(,0,0)).
163    
164            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
165            * man/sparseLU-class.Rd: ditto
166    
167            * R/dgCMatrix.R (determinant): method building on lu()
168            * R/sparseMatrix.R, Matrix.R, ...: ditto
169    
170            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
171    
172    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
175            pattern matrices.
176    
177    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * src/dense.c (dense_to_Csparse): all declarations *before*
180            R_CheckStack(); needed e.g. for ancient gcc 2.96.
181    
182    
183    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * DESCRIPTION (Version): 0.999375-9 --- need to release
186            for R-devel (and R 2.7.0 alpha soon).
187    
188            * R/AllClass.R: drop "double" from "atomicVector" class union
189    
190            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
191            * R/dgeMatrix.R: ditto
192    
193            * R/sparseMatrix.R (summary): count NAs
194    
195            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
196    
197    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
200            order to become compatible to new R 2.7.0 base::rcond().
201    
202    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
205    
206            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
207    
208            * inst/test-tools.R (isValid): new utility, used much in
209            * tests/simple.R:
210    
211            * man/BunchKaufman-methods.Rd: added too
212    
213    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/dsyMatrix.R: add BunchKaufman() methods.
216            * R/dspMatrix.R:
217    
218            * src/init.c: add dsyMatrix_trf
219    
220    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
221    
222            * DESCRIPTION (Version): release 0.999375-7
223            * src/CHMfactor.c (CHMfactor_update): fix
224    
225    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
228            internal_chm_factor().
229    
230            * R/AllGeneric.R: do *not* define a "chol" generic
231                    (but rather use the implicit one *without* making pivot
232                    part of the signature)
233            * R/*.R: drop the 'pivot' from chol's signature and make
234                    'pivot=FALSE' a default argument of method definitions.
235    
236            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
237            version of Matrix
238    
239    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
242    
243            * R/sparseMatrix.R (is.na): new simple method
244            * R/denseMatrix.R (is.na): ditto.
245    
246            * R/diagMatrix.R (.symDiagonal): newly exported utility.
247    
248            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
249    
250            * src/UFsparse_download.sh: -->
251            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
252    
253    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
256            functionality; barely tested in
257            * tests/factorizing.R
258    
259            * src/Csparse.c (diag_tC): new functionality to enable faster
260            determinant(<dsCMatrix>, .) in
261            * R/dsCMatrix.R
262    
263    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
264    
265            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
266              src/CHMfactor.c, src/CHMfactor.h,
267              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
268              Log-determinant of the parent matrix from a CHMfactor object as
269              chm_factor_ldetL2; documentation and support
270    
271    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
274    
275    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
278            warning.
279    
280    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
283    
284            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
285              <diagonal> o <sparse_triangular>
286              setAs(., "nMatrix") added.
287    
288            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
289    
290            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
291                    new argument 'checkDense = FALSE'.
292    
293    
294    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
297            back-permutation of the matrix exponential.
298    
299            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
300    
301            * DESCRIPTION (Date,Version): ready to release 0.999375-5
302    
303            * tests/simple.R: testing diagN2U
304    
305    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/Auxiliaries.R (diagN2U): interface to
308    
309            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
310    
311            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
312    
313    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * src/chm_common.c (chm_diagN2U): new utility.
316    
317            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
318            make use of chm_diagN2U() and hence now preserve triangularity and
319            unit-triangularity.
320    
321            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
322    
323    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
326    
327            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
328            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
329    
330            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
331    
332            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
333    
334            * src/chm_common.c (AS_CHM_FINISH): add note about problem
335            for triangular (diag = "U").
336    
337    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
340            * R/bind.R:  .Call(dense_to_Csparse, *)
341    
342    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * R/Matrix.R (Matrix): no longer use coercions to specific classes
345                    (since we are discouraging them in user code).
346    
347            * tests/*.R: also replaces coercions to specific classes by
348            coercions to super classes.
349    
350            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
351    
352    
353    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
356    
357            * src/dense.c (dense_band): generalized from ddense_band
358    
359            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
360              now for "denseMatrix" (instead of just "ddense*"); much
361              simplified setMethod()s for these.
362    
363            * src/dense.c (dense_to_symmetric): generalized from ddense_*
364    
365    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
368            version of as(*, "symmetricMatric").
369    
370            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
371            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
372    
373    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/Matrix.R (subset.ij): utility, as first step to faster
376               M [ <ij-matrix> ] indexing.
377    
378            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
379    
380            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
381            for more efficient symmpart() and skewpart() methods.
382    
383            * src/Mutils.c (equal_string_vectors): utility
384    
385            * src/dense.c (ddense_to_symmetric): new function used in
386    
387            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
388    
389            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
390            order to match the generic (and evade .local(..)).
391    
392            * R/dsCMatrix.R: dgC -> dsC: use C code!
393    
394            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
395            as per TODO
396    
397            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
398    
399            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
400    
401    
402    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
405    
406            * R/Auxiliaries.R (non0.i): take out of non0ind
407    
408            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
409            make tril(), triu(), band() work for "matrix" and all "dense*"
410    
411            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
412            * tests/simple.R: test the fix above
413    
414            * R/sparseMatrix.R ([): simplification: no coerce to <general>
415                    before we use as(., <Tsparse>)[...] anyway
416    
417            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
418    
419            * R/triangularMatrix.R (isTriangular): methods for all subclasses
420            instead of "triangularMatrix" -- just to disambiguate
421    
422    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
425            * tests/indexing.R: example that fails above
426    
427    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
430            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
431                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
432    
433            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
434            * src/Tsparse.h, init.c: ditto
435            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
436                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
437            * R/sparseMatrix.R (isTriangular): hence simplified
438    
439    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/Ops.R (.Arith.Csparse): new utility factored out of former
442              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
443    
444    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
447    
448            * inst/test-tools.R (isOrthogonal): new function; also file restructured
449    
450    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
453            coercion to "nMatrix" and "pMatrix"
454    
455            * R/AllClass.R: "Schur" class;  "number" class union
456            * man/number-class.Rd:
457            * man/Schur-class.Rd:
458    
459            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
460            (.simpleSchur): Schur() method for diagonal matrices
461            (.triSchur):    Schur() method for triangular matrices
462            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
463    
464    
465    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
468    
469    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
472                    in order to ensure 'system = *' is not lost;
473                    formals()$system instead of cut&paste.
474            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
475    
476    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * DESCRIPTION (Date): make ready for release --> 0.999375-4
479    
480            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
481    
482    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
485                    and hence does as.vector(.).
486            * man/pMatrix-class.Rd: docs
487            * R/sparseMatrix.R: fix for printing "integer sparse"
488    
489            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
490    
491            * R/Matrix.R and others: use "exact" function argument list for
492                    both "["   : (x, i,j, ..., drop)
493                    and  "[<-" : (x, i,j, ..., value)
494    
495            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
496            * R/Tsparse.R (replTmat):    ditto
497            * R/diagMatrix.R (replDiag): ditto
498            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
499            * tests/indexing.R: testing the above
500    
501    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
502    
503            * R/sparseMatrix.R (cov2cor): method for sparse matrices
504    
505            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
506    
507            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
508    
509            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
510    
511    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * R/Matrix.R: "generic" cov2cor() method
514    
515            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
516                    speed up Q %*% D %*% t(Q)
517            * tests/dpoMatrix.R: test nearPD()
518    
519    2007-12-05  Doug Bates and Martin Maechler
520    
521            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
522            stats::xtabs() allowing to create sparse matrices.
523    
524    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
527    
528    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
529    
530            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
531    
532    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * R/LU.R: solve() method for "denseLU"
535    
536    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
538            * DESCRIPTION (Version): 0.999375-3 preparing for release
539    
540            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
541    
542            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
543    
544    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
545    
546            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
547              thanks to Kasper Kristensen.
548            * tests/matprod.R: regression test for that.
549    
550    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
551    
552            * [r4778] R/AllGeneric.R: Check R version before defining generics for
553              primitives
554    
555    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
556    
557            * R/denseMatrix.R (rcond): method
558            * R/sparseQR.R (rcond): method, use x or t(x)
559    
560    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
563            matrices.
564            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
565    
566            * man/rcond.Rd: mention the more general definition, and add
567            example for non-square matrices.
568    
569            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
570    
571    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
574    
575    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
578            * tests/indexing.R: add new regression for the above cases.
579    
580    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * src/Mutils.h (__sun): clause for alloca.h on Solaris
583    
584    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * DESCRIPTION (Date, Version): 0.999375-2
587    
588    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
589    
590            * R/HBMM.R (readMM): make work for pattern matrices as well
591    
592    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
593    
594            * [r4730] src/Mutils.h: declare alloca
595            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
596              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
597              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
598              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
599              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
600              methods; switch writeMM to use CHOLMOD code; repair readMM
601    
602    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
604            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
605            Oehlschlaegel's ... result type still to be discussed!
606    
607    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * man/image-methods.Rd: new, combining all image() methods
610    
611    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
612    
613            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
614            to work via dgC...
615    
616            * R/Matrix.R (Matrix): special treatment for "table" (S3)
617    
618    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * R/dgTMatrix.R (image): change defaults to
621                    aspect = "iso", colorkey = FALSE
622    
623    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
624    
625            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
626            must copy its *expanded* x slot before LAPACK call.
627    
628            * tests/matprod.R: test the last days' changes.
629    
630    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
631    
632            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
633              as well as in sources
634            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
635              Lapack call
636    
637    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
638    
639            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
640                    ("Matrix", "matrix") which is needed in some cases.
641            Ditto for solve().
642    
643            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
644            infinite recursion in dispatch for some cases.
645    
646    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
647    
648            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
649              so pointers match
650    
651    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * DESCRIPTION (Date): set ready for release -- 0.999375-1
654    
655    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
656    
657            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
658              src/chm_common.c, src/chm_common.h: Change API for
659              numeric_as_chm_dense and N_AS_CHM_DN
660    
661    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
662    
663            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
664            * tests/matprod.R: regr.test for it
665    
666    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
669            * tests/group-methods.R: and regression-test it
670    
671    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
672    
673            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
674              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
675              triplet_to_sparse, documentation, use typedefs
676    
677    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
678    
679            * man/dpoMatrix-class.Rd: added 'corMatrix' example
680    
681            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
682            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
683            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
684    
685            * R/lsparseMatrix.R: bug fix in "all" method
686            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
687    
688            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
689            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
690                    + matrix |-> nMatrix coercion
691            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
692            * man/pMatrix-class.Rd: ditto
693    
694            * R/Matrix.R (Summary): method for non-dMatrix
695    
696            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
697            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
698                    test all Summary methods.
699    
700    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
701    
702            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
703    
704    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
705    
706            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
707    
708            * R/pMatrix.R (t?crossprod): methods for pMatrix
709    
710    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
711    
712            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
713    
714    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
715    
716            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
717              trying to fix a subtle bug - which has been somewhere else.
718    
719    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
720    
721            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
722              solve the bug
723    
724    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
725    
726            * src/dgCMatrix.c (compressed_to_TMatrix):
727    
728    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
729    
730            * src/Csparse.c (Rsparse_validate): new, to have some validity
731            checking for RsparseMatrix
732            * src/dgCMatrix.c (xRMatrix_validate): ditto
733            * src/dtCMatrix.c (tRMatrix_validate): ditto
734    
735    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
736    
737            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
738              lgRMatrix
739            * [r4568] DESCRIPTION: Prepare for bug-fix release
740            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
741              for declaration of cholmod_symmetry
742    
743    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
744    
745            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
746            release.
747    
748    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
749    
750            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
751              functions - no longer used
752            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
753              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
754              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
755              Alloca
756    
757    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
758    
759            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
760              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
761              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
762              src/t_gCMatrix_colSums.c: more R_CheckStack()s
763    
764    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
765    
766            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
767              the required amount of memory then call M_numeric_as_chm_dense.
768            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
769              (like Calloc but calling alloca)
770    
771    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
772    
773            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
774            and extended with more sophisticated 'col.names' option.
775            * NAMESPACE: export  printSparseMatrix()
776            * man/printSpMatrix.Rd: document, incl. examples
777    
778    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
779    
780            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
781              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
782              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
783    
784    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
785    
786            * DESCRIPTION (Version): 0.99875-4
787    
788            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
789            some dimnames perservation.
790    
791            * R/dsTMatrix.R (t-method): keep dimnames
792            * R/dtTMatrix.R:  ditto
793    
794            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
795            and ncol(.) < 10
796    
797            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
798            from Mutils.h
799    
800            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
801            e.g. in as(<ngCMatrix>, "matrix")
802    
803    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
804    
805            * [r4529] .: Create a branch for the API changes from the 0.99875
806              series to the 0.999375 series
807            * [r4530] DESCRIPTION, inst/include/Matrix.h,
808              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
809              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
810              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
811              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
812              as_cholmod_x functions
813    
814    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
815    
816            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
817              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
818              to Comparisons
819    
820    >>>>>>> .merge-right.r4561
821    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
822    
823            * DESCRIPTION (Version): 0.99875-3 ready to be released.
824    
825            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
826    
827            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
828            that should also work in a future version of R.
829    
830    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
831    
832            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
833    
834            * R/sparseVector.R: more *sparseVector coercions, notably for
835            non - double ones.
836    
837    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
838    
839            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
840              notably the new ones building on the new .Call(.)s:
841    
842            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
843            all 4 of [dlin]gCMatrix_colSums().
844    
845    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
846    
847            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
848            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
849              result
850    
851    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
852    
853            * R/kronecker.R: fix typo (could lead to inf.recursion)
854            * test/simple.R: testing that
855    
856            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
857            method as well (which can have arguments, show() can't).
858    
859    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
860    
861            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
862              added dgCMatrix_colSums for [col,row][Sums,Means]
863    
864    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
865    
866            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
867              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
868              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
869            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
870              class
871            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
872              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
873              row names to store the levels - duh!  Added an example.
874    
875    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
876    
877            * src/Csparse.c (Csparse_validate): check for *repeated* entries
878            thanks to example from Christian Buchta; with a test here:
879            * tests/simple.R:
880    
881    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
882    
883            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
884            of colSums(*, sparseResult = TRUE)
885    
886    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
887    
888            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
889            'na.rm = FALSE' as "everywhere" else in R.
890    
891    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
892    
893            * [r4421] src/CSparse_install.sh: Modify for new organization of
894              CSparse package
895            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
896              SuiteSparse
897            * [r4426] src/Makefile: add ./UFconfig to the include path for
898              compilation
899            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
900            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
901              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
902    
903    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
904    
905            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
906            * R/sparseMatrix.R (prSpMatrix): now gives a message about
907            suppressed column names.
908    
909    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
910    
911            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
912              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
913              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
914              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
915              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
916              Remove warnings after change to const char* CHAR
917    
918    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
919    
920            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
921              type of M_cholmod_ssmult
922    
923    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
924    
925            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
926              src/init.c: Yet another cholmod export - cholmod_ssmult
927    
928    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
929    
930            * NAMESPACE: exported drop0(), since
931            * man/drop0.Rd: I have seen several cases, I really wanted to use
932            it, so our users may want too.
933    
934    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
935    
936            * man/colSums.Rd: separately document colSums() etc, since these
937            have the extra argument 'sparseResult'.
938    
939    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
940    
941            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
942            * man/spMatrix.Rd: docu., including examples
943    
944            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
945            in order to make colMeans() etc fast *and* correct.
946            * R/sparseVector.R (replSPvec): "[<-" functionality for
947            sparseVectors; tested in
948            * tests/simple.R:
949    
950    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
951    
952            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
953            (very) sparse Matrices; output similar to Matlab's print().
954    
955    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
956    
957            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
958            0-based, indices (Jose Quesada <quesada@gmail.com>).
959    
960    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
961    
962            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
963    
964    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
965    
966            * R/Auxiliaries.R (sparsapply): new utility, much faster than
967            tapply1() for large sparse matrices.
968    
969    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
970    
971            * R/Matrix.R (dim<-): reshape now via sparseVector.
972    
973            * R/sparseVector.R: methods and function for
974            * R/AllClass.R: new "sparseVector" class and daughters.
975            * NAMESPACE: export new classes
976    
977    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
978    
979            * DESCRIPTION (Version): 0.99875-1
980            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
981    
982    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
983    
984            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
985            indexing
986            * tests/indexing.R: test set for that.
987    
988    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
989    
990            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
991            entries.
992            * tests/indexing.R(out): add regression test for it
993    
994    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
995    
996            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
997            name for "!" method definitions.
998    
999    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1000    
1001            * R/Tsparse.R (intI): new utility, used for "[" :
1002                    Cleanup up there, and fixes for duplicated indices - more TODO!
1003    
1004            * tests/indexing.R(out): more tests
1005    
1006    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1007    
1008            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1009            code that is now part of the R Lapack library.
1010    
1011            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1012            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1013    
1014    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1015    
1016            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1017    
1018    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1019    
1020            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1021            up with extraneous names '0'...'<n-1>'
1022    
1023    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1024    
1025            * R/dgTMatrix.R (mat2dgT): care about NAs
1026    
1027    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1028    
1029            * R/kronecker.R: triangularity preserving methods
1030    
1031    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1032    
1033            * R/kronecker.R: new file collecting kronecker() methods in one
1034                    place.  Goal: become much faster!
1035    
1036    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1037    
1038            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1039            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1040            can be much faster.
1041    
1042            * tests/matprod.R: add regression tests for these (upper & lower).
1043    
1044    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1045    
1046            * R/Matrix.R (diff): method for our Matrices.
1047    
1048            * R/sparseMatrix.R (isDiagonal): check dim()!
1049    
1050    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1051    
1052            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1053            proposal from Tamas Papp.
1054    
1055    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1056    
1057            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1058    
1059            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1060            rather define and export  cBind() and rBind() only.
1061            --> useRs *must* change code that used to have cbind()/rbind() !!
1062    
1063            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1064            * R/bind.Rout.save: ditto
1065    
1066    2007-02-16  Douglas Bates  <bates@r-project.org>
1067    
1068            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1069            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1070            const modifier on declaration of the array 'valid'
1071    
1072    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1073    
1074            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1075    
1076    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1077    
1078            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1079    
1080            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1081            * tests/simple.R: test the above and some of these coercions:
1082    
1083            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1084                    be careful to avoid infinite recursion, using new coercions in
1085            * R/ngCMatrix.R and nsC... and ntC...
1086            * R/lsparseMatrix.R: ditto
1087    
1088            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1089    
1090            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1091            * R/Rsparse.R: reactivate .Call()s
1092    
1093            * tests/Class+Meth.R: a bit more on actual classes
1094    
1095    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1096    
1097            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1098    
1099    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1100    
1101            * DESCRIPTION (Version): 0.9975-10 to upload
1102    
1103            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1104            specific classes less unconditionally.
1105    
1106            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1107    
1108            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1109    
1110            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1111            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1112            R_to_CMatrix segfaults on one platform.
1113            Eliminate most coercion method to *specific* classes, and replace
1114            with virtual classes coercions.
1115    
1116    
1117    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1118    
1119            * src/init.c: export the CHM...._validate() placeholders, since
1120            they *are* called.
1121    
1122            * tests/Class+Meth.R (classCanCoerce): and starting to test
1123            all as(<from>, <to>)
1124    
1125    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1126    
1127            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1128            * tests/indexing.R: tested now
1129            * tests/indexing.Rout.save: updated
1130    
1131            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1132            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1133            appropriate.
1134    
1135            * NAMESPACE: export a trivial
1136            * R/Matrix.R: drop() Matrix-method
1137    
1138            * R/AllClass.R: moved all prototypes to virtual super classes.
1139    
1140            * R/Rsparse.R: many more coercions to have less exceptions in
1141            * tests/Class+Meth.R:
1142    
1143            * R/Ops.R (Compare): tweak for case with NA
1144            * tests/simpl.R: hence another 'FIXME' eliminated
1145    
1146    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1147    
1148            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1149            objects.
1150    
1151            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1152              and more of "!", "&", "|", all, any; coercions
1153    
1154            * R/Rsparse.R: many coercions (which enable quite a few other
1155            methods), thanks to enhancements in
1156            * src/dgCMatrix.c (R_to_CMatrix): new, and
1157            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1158            symmetric & triangular and ..RMatrix objects.
1159    
1160            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1161            renamed file from src/dsTMatrix.c;
1162            now dealing with symmetric and triangular Tsparse coercions, both
1163            to dense and general.
1164    
1165    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1166    
1167            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1168    
1169            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1170            where sensible when the <numeric> is of length > 1.
1171    
1172    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1173    
1174            * R/Matrix.R ([<-): for M[] <- value: fix length
1175    
1176    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1177    
1178            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1179            * R/ndenseMatrix.R: new coercions n* -> l*
1180    
1181    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1182    
1183            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1184    
1185            * R/Ops.R ("Logic"): and other "Ops", many updates
1186    
1187    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1188    
1189            * src/Mutils.h (SET_DimNames): new utility
1190    
1191            * R/Auxiliaries.R (nnzero): improved and now exported via
1192    
1193            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1194    
1195    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1196    
1197            * R/diagMatrix.R (!): fix typo.
1198    
1199    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1200    
1201            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1202                    allow to pass class definition --> speedup
1203            * R/sparseMatrix.R: apply the above
1204    
1205            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1206    
1207            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1208            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1209            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1210    
1211            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1212    
1213            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1214            and use it for "sparse*" as well, since it's faster than the
1215            as_Csparse(.) way.
1216    
1217    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1218    
1219            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1220    
1221    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1222    
1223            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1224            as method for   M[ ij ] <- v
1225            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1226    
1227            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1228            FALSE answer
1229    
1230            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1231            * tests/indexing.R: test it, and some of the above
1232    
1233    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1234    
1235            * R/Auxiliaries.R (is_duplicatedT): new utility
1236    
1237    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1238    
1239            * src/init.c (R_init_Matrix): export cholmod_scale
1240    
1241    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1242    
1243            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1244            base::as.matrix to (x, ...)
1245    
1246    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1247    
1248            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1249            file; start using "Logic", hence
1250    
1251            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1252            * NAMESPACE: import and export "Logic"
1253    
1254    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1255    
1256            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1257            only needed previously to R version 2.5.0.
1258    
1259    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1260    
1261            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1262    
1263            * R/Tsparse.R (replTmat): fix subassignment of triangular
1264            * R/Csparse.R (replCmat): ditto
1265            * tests/indexing.R: more tests, incl the above fix
1266    
1267    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1268    
1269            * R/Auxiliaries.R (drop0): extend for non CSparse
1270            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1271    
1272            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1273                    use uplo correctly (!); other places: use uplo_P() macro
1274    
1275            * R/Csparse.R (replCmat): call diagU2N() when needed
1276            * R/Tsparse.R (replTmat): ditto
1277    
1278            * src/dtCMatrix.c (tCMatrix_validate): new
1279            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1280            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1281    
1282            * R/diagMatrix.R (replDiag): to use in [<-
1283    
1284    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1285    
1286            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1287                    also more general diagU2N().
1288    
1289    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1290    
1291            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1292            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1293    
1294    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1295    
1296            * tests/bind.R: a few more cases
1297            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1298    
1299            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1300            * R/ddenseMatrix.R (cbind2/rbind2)
1301            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1302            * tests/indexing.R
1303            * tests/indexing.Rout.save: updated
1304    
1305    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1306    
1307            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1308            * tests/indexing.R
1309    
1310    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1311    
1312            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1313            align with proper position of "0", i.e., right for integers.
1314            argument 'align' by default is "fancy".
1315    
1316    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1317    
1318            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1319            * R/Csparse.R: and fix "Compare" for more cases.
1320            * tests/Class+Meth.R: test some of these (m == m, m != m)
1321    
1322    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1323    
1324            * R/lsparseMatrix.R: all() and any() methods
1325            * R/ldenseMatrix.R:      ditto
1326            * NAMESPACE, R/Matrix.R: ditto
1327    
1328            * man/all-methods.Rd: document them minimally
1329    
1330            * tests/simple.R: add a few examples for these
1331    
1332    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1333    
1334            * R/Tsparse.R ([): fix long standing typo in symmetric case
1335            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1336    
1337    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1338    
1339            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1340            to LL before converting to a sparse matrix. (The LDL form can be
1341            converted to a sparse matrix but it is implicitly a unit
1342            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1343    
1344    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1345    
1346            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1347    
1348    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1349    
1350            * DESCRIPTION (Version): updated -> release 0.9975-7
1351            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1352    
1353    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1354    
1355            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1356    
1357    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1358    
1359            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1360            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1361            is exactly singular.
1362    
1363    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1364    
1365            * DESCRIPTION (Date): updated -> release 0.9975-6
1366    
1367    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1368    
1369            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1370            now returns symmetric.
1371    
1372            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1373    
1374            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1375            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1376    
1377            * R/Auxiliaries.R (.type.kind): added
1378    
1379    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1380    
1381            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1382            running src/CSparse_install.sh
1383    
1384            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1385    
1386    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1387    
1388            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1389            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1390    
1391            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1392    
1393            * tests/Class+Meth.R (tstMatrixClass): now assure
1394            the (important in method programming) property :
1395    
1396                    ###>>  Every "Matrix" is either
1397                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1398    
1399                    (where "*" stands for "Matrix")
1400    
1401            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1402    
1403            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1404            * tests/validObj.R: checks for "comparison"
1405    
1406            * R/sparseMatrix.R ([): improved indexing for sparse;
1407                    trying to keep <symmetric>[ n, n] symmmetric
1408    
1409            * tests/indexing.R: indexing for logical sparse now ok
1410    
1411    
1412    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1413    
1414            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1415    
1416            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1417    
1418    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1419    
1420            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1421    
1422            * tests/simple.R: validObject() checking the above.
1423    
1424            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1425            replacing both dgCMatrix_validate and lgCM*.
1426    
1427            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1428            fix dimnames setting in other places.
1429            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1430    
1431    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1432    
1433            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1434    
1435            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1436            symmetry test, via
1437            * R/Auxiliaries.R (.as.dgC.0.factors):
1438    
1439    2006-11-01  Douglas Bates  <bates@r-project.org>
1440    
1441            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1442            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1443            <CsparseMatrix>) added
1444    
1445    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1446    
1447            * tests/matprod.R: add a variation of Harri's example
1448    
1449            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1450            recursive infinitely.
1451    
1452            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1453    
1454            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1455    
1456    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1457    
1458            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1459            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1460            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1461            satisfy the above test.
1462    
1463    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1464    
1465            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1466    
1467            * R/dgCMatrix.R: solve(a, b="missing") based on
1468            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1469            RHS = NULL.
1470    
1471            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1472            add more (needed) [t]crossprod() methods.
1473    
1474            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1475    
1476            * R/Auxiliaries.R (as_CspClass): cleanup
1477            (drop0): internal utility for "Csparse_drop(*, 0)"
1478            (.bail.out.2): encourage active feedback
1479    
1480    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1481    
1482            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1483    
1484            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1485            non-valid or 'sorted' case).
1486    
1487            * R/dsparseMatrix.R: add "chol" method.
1488            * R/ddenseMatrix.R: ditto
1489    
1490            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1491            * NAMESPACE (Ops)
1492            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1493            coercion; deprecating direct lower level coercions.
1494    
1495            * R/*.R (seq): use seq_len() and seq_along() where possible.
1496    
1497    
1498    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1499    
1500            * DESCRIPTION (Version): 0.9975-5 ready for release
1501    
1502  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1503    
1504          * src/init.c (R_init_Matrix): export more cholmod CCallable functions.          * src/init.c (R_init_Matrix): export more cholmod CCallable functions.

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