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revision 1577, Mon Sep 18 21:01:45 2006 UTC revision 2202, Mon Jun 9 21:36:21 2008 UTC
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1    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dtCMatrix.R: faster dgC* -> dtC* method
4            * tests/Simple.R: (hence removed "FIXME")
5    
6            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
7            which can be be turned off for possible speed gains.
8    
9    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
12    
13            * R/not.R: fix !<ldiMatrix>
14            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
15    
16            * R/diagMatrix.R (Ops): fix one-off thinko in
17            <diagonal> o <numeric> methods
18    
19            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
20    
21    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
24            * tests/Simple.R: testing the above
25    
26    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
29    
30    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
33            * NAMESPACE (unname): finally exported
34    
35    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/Auxiliaries.R (cholMat): possibly keep packed
38    
39            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
40            for R < 2.7.0.
41    
42            * R/Tsparse.R ([): for triangularMatrix, check if result may be
43            triangular.
44            * tests/indexing.R: regression test
45    
46    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
49            * R/Ops.R: more methods, for lMatrix/nMatrix
50    
51    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/expm.R: new file for all expm() methods; notably new ones for
54            diagonal*, triangular*, symmetric* and also simple "matrix".
55    
56    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
59    
60            * inst/test-tools.R (assert.EQ.mat): better message when not equal
61    
62            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
63    
64            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
65            [dl]denseMatrix {identical slots; but more logical method dispatch}
66    
67    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
70    
71            * R/diagMatrix.R (determinant): method
72    
73    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
76    
77            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
78    
79            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
80            its diagonal
81    
82    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
85    
86            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
87    
88            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
89    
90            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
91    
92    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
95    
96            * R/Ops.R (.do.Logic.lsparse): fix NA case
97    
98            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
99    
100            * R/Auxiliaries.R (nnzero): fix special cases, using
101            * R/Auxiliaries.R (indDiag): new utility
102            * R/Auxiliaries.R (indTri): new argument 'diag'
103    
104            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
105    
106    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
109    
110            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
111            ".tCMatrix" triangular matrix.
112    
113            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
114            'clx' can be class *or* class representation.
115            (nnzSparse): new.
116            (non0ind): new 'xtendSymm' argument; used in
117            * R/Ops.R:
118    
119            * R/pMatrix.R: more efficient determinant() method
120    
121    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
124            * [disactivated] NAMESPACE: export(det)
125    
126            * R/diagMatrix.R (mkDiag): new substitute for diag()
127    
128            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
129            (as0, as1): new utility.
130    
131            * R/Csparse.R (diag, band): need diagU2N()
132    
133            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
134    
135            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
136    
137            * R/Ops.R (Compare): fix <nsp> o <nsp> case
138    
139            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
140    
141    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/Auxiliaries.R (signPerm): new utility for
144            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
145    
146            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
147            since we have our own error handler (and can use tryCatch() from R).
148    
149    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
152    
153            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
154            when not positive definite.
155    
156            * R/Auxiliaries.R (asTri): new auxiliary
157            (non0.i): make *much* faster for Tsparse with many non-zero
158            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
159    
160            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
161            test-tools.R , see below
162    
163            * R/dMatrix.R: fix "Summary" method: + diagU2N()
164    
165            * NAMESPACE, R/Matrix.R: add mean() method
166    
167    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
170            cold-hot colors; try *changed* default useAbs = FALSE
171            * man/image-methods.Rd:  nice examples
172    
173    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * inst/test-tools.R (checkMatrix): new function for modularizing part
176            of tstMatrixClass() in tests/Class+Meth.R
177    
178            * R/dsCMatrix.R: coercion from "matrix"
179            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
180    
181            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
182            add test for as(matrix(,0,0), <class>)
183    
184    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
187            work as determinant(matrix(,0,0)).
188    
189            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
190            * man/sparseLU-class.Rd: ditto
191    
192            * R/dgCMatrix.R (determinant): method building on lu()
193            * R/sparseMatrix.R, Matrix.R, ...: ditto
194    
195            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
196    
197    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
200            pattern matrices.
201    
202    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * src/dense.c (dense_to_Csparse): all declarations *before*
205            R_CheckStack(); needed e.g. for ancient gcc 2.96.
206    
207    
208    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * DESCRIPTION (Version): 0.999375-9 --- need to release
211            for R-devel (and R 2.7.0 alpha soon).
212    
213            * R/AllClass.R: drop "double" from "atomicVector" class union
214    
215            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
216            * R/dgeMatrix.R: ditto
217    
218            * R/sparseMatrix.R (summary): count NAs
219    
220            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
221    
222    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
225            order to become compatible to new R 2.7.0 base::rcond().
226    
227    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
230    
231            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
232    
233            * inst/test-tools.R (isValid): new utility, used much in
234            * tests/simple.R:
235    
236            * man/BunchKaufman-methods.Rd: added too
237    
238    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/dsyMatrix.R: add BunchKaufman() methods.
241            * R/dspMatrix.R:
242    
243            * src/init.c: add dsyMatrix_trf
244    
245    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
246    
247            * DESCRIPTION (Version): release 0.999375-7
248            * src/CHMfactor.c (CHMfactor_update): fix
249    
250    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
253            internal_chm_factor().
254    
255            * R/AllGeneric.R: do *not* define a "chol" generic
256                    (but rather use the implicit one *without* making pivot
257                    part of the signature)
258            * R/*.R: drop the 'pivot' from chol's signature and make
259                    'pivot=FALSE' a default argument of method definitions.
260    
261            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
262            version of Matrix
263    
264    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
267    
268            * R/sparseMatrix.R (is.na): new simple method
269            * R/denseMatrix.R (is.na): ditto.
270    
271            * R/diagMatrix.R (.symDiagonal): newly exported utility.
272    
273            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
274    
275            * src/UFsparse_download.sh: -->
276            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
277    
278    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
281            functionality; barely tested in
282            * tests/factorizing.R
283    
284            * src/Csparse.c (diag_tC): new functionality to enable faster
285            determinant(<dsCMatrix>, .) in
286            * R/dsCMatrix.R
287    
288    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
289    
290            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
291              src/CHMfactor.c, src/CHMfactor.h,
292              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
293              Log-determinant of the parent matrix from a CHMfactor object as
294              chm_factor_ldetL2; documentation and support
295    
296    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
299    
300    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
303            warning.
304    
305    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
308    
309            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
310              <diagonal> o <sparse_triangular>
311              setAs(., "nMatrix") added.
312    
313            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
314    
315            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
316                    new argument 'checkDense = FALSE'.
317    
318    
319    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
322            back-permutation of the matrix exponential.
323    
324            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
325    
326            * DESCRIPTION (Date,Version): ready to release 0.999375-5
327    
328            * tests/simple.R: testing diagN2U
329    
330    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/Auxiliaries.R (diagN2U): interface to
333    
334            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
335    
336            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
337    
338    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * src/chm_common.c (chm_diagN2U): new utility.
341    
342            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
343            make use of chm_diagN2U() and hence now preserve triangularity and
344            unit-triangularity.
345    
346            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
347    
348    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
351    
352            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
353            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
354    
355            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
356    
357            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
358    
359            * src/chm_common.c (AS_CHM_FINISH): add note about problem
360            for triangular (diag = "U").
361    
362    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
365            * R/bind.R:  .Call(dense_to_Csparse, *)
366    
367    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * R/Matrix.R (Matrix): no longer use coercions to specific classes
370                    (since we are discouraging them in user code).
371    
372            * tests/*.R: also replaces coercions to specific classes by
373            coercions to super classes.
374    
375            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
376    
377    
378    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
381    
382            * src/dense.c (dense_band): generalized from ddense_band
383    
384            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
385              now for "denseMatrix" (instead of just "ddense*"); much
386              simplified setMethod()s for these.
387    
388            * src/dense.c (dense_to_symmetric): generalized from ddense_*
389    
390    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
393            version of as(*, "symmetricMatric").
394    
395            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
396            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
397    
398    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/Matrix.R (subset.ij): utility, as first step to faster
401               M [ <ij-matrix> ] indexing.
402    
403            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
404    
405            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
406            for more efficient symmpart() and skewpart() methods.
407    
408            * src/Mutils.c (equal_string_vectors): utility
409    
410            * src/dense.c (ddense_to_symmetric): new function used in
411    
412            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
413    
414            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
415            order to match the generic (and evade .local(..)).
416    
417            * R/dsCMatrix.R: dgC -> dsC: use C code!
418    
419            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
420            as per TODO
421    
422            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
423    
424            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
425    
426    
427    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
430    
431            * R/Auxiliaries.R (non0.i): take out of non0ind
432    
433            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
434            make tril(), triu(), band() work for "matrix" and all "dense*"
435    
436            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
437            * tests/simple.R: test the fix above
438    
439            * R/sparseMatrix.R ([): simplification: no coerce to <general>
440                    before we use as(., <Tsparse>)[...] anyway
441    
442            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
443    
444            * R/triangularMatrix.R (isTriangular): methods for all subclasses
445            instead of "triangularMatrix" -- just to disambiguate
446    
447    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
450            * tests/indexing.R: example that fails above
451    
452    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
455            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
456                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
457    
458            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
459            * src/Tsparse.h, init.c: ditto
460            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
461                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
462            * R/sparseMatrix.R (isTriangular): hence simplified
463    
464    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * R/Ops.R (.Arith.Csparse): new utility factored out of former
467              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
468    
469    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
472    
473            * inst/test-tools.R (isOrthogonal): new function; also file restructured
474    
475    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
478            coercion to "nMatrix" and "pMatrix"
479    
480            * R/AllClass.R: "Schur" class;  "number" class union
481            * man/number-class.Rd:
482            * man/Schur-class.Rd:
483    
484            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
485            (.simpleSchur): Schur() method for diagonal matrices
486            (.triSchur):    Schur() method for triangular matrices
487            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
488    
489    
490    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
493    
494    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
497                    in order to ensure 'system = *' is not lost;
498                    formals()$system instead of cut&paste.
499            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
500    
501    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
502    
503            * DESCRIPTION (Date): make ready for release --> 0.999375-4
504    
505            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
506    
507    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
508    
509            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
510                    and hence does as.vector(.).
511            * man/pMatrix-class.Rd: docs
512            * R/sparseMatrix.R: fix for printing "integer sparse"
513    
514            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
515    
516            * R/Matrix.R and others: use "exact" function argument list for
517                    both "["   : (x, i,j, ..., drop)
518                    and  "[<-" : (x, i,j, ..., value)
519    
520            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
521            * R/Tsparse.R (replTmat):    ditto
522            * R/diagMatrix.R (replDiag): ditto
523            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
524            * tests/indexing.R: testing the above
525    
526    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
527    
528            * R/sparseMatrix.R (cov2cor): method for sparse matrices
529    
530            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
531    
532            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
533    
534            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
535    
536    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
538            * R/Matrix.R: "generic" cov2cor() method
539    
540            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
541                    speed up Q %*% D %*% t(Q)
542            * tests/dpoMatrix.R: test nearPD()
543    
544    2007-12-05  Doug Bates and Martin Maechler
545    
546            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
547            stats::xtabs() allowing to create sparse matrices.
548    
549    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
552    
553    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
554    
555            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
556    
557    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/LU.R: solve() method for "denseLU"
560    
561    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * DESCRIPTION (Version): 0.999375-3 preparing for release
564    
565            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
566    
567            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
568    
569    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
572              thanks to Kasper Kristensen.
573            * tests/matprod.R: regression test for that.
574    
575    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
576    
577            * [r4778] R/AllGeneric.R: Check R version before defining generics for
578              primitives
579    
580    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * R/denseMatrix.R (rcond): method
583            * R/sparseQR.R (rcond): method, use x or t(x)
584    
585    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
588            matrices.
589            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
590    
591            * man/rcond.Rd: mention the more general definition, and add
592            example for non-square matrices.
593    
594            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
595    
596    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
599    
600    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
601    
602            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
603            * tests/indexing.R: add new regression for the above cases.
604    
605    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * src/Mutils.h (__sun): clause for alloca.h on Solaris
608    
609    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * DESCRIPTION (Date, Version): 0.999375-2
612    
613    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/HBMM.R (readMM): make work for pattern matrices as well
616    
617    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
618    
619            * [r4730] src/Mutils.h: declare alloca
620            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
621              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
622              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
623              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
624              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
625              methods; switch writeMM to use CHOLMOD code; repair readMM
626    
627    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
630            Oehlschlaegel's ... result type still to be discussed!
631    
632    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * man/image-methods.Rd: new, combining all image() methods
635    
636    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
639            to work via dgC...
640    
641            * R/Matrix.R (Matrix): special treatment for "table" (S3)
642    
643    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * R/dgTMatrix.R (image): change defaults to
646                    aspect = "iso", colorkey = FALSE
647    
648    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
649    
650            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
651            must copy its *expanded* x slot before LAPACK call.
652    
653            * tests/matprod.R: test the last days' changes.
654    
655    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
656    
657            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
658              as well as in sources
659            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
660              Lapack call
661    
662    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
665                    ("Matrix", "matrix") which is needed in some cases.
666            Ditto for solve().
667    
668            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
669            infinite recursion in dispatch for some cases.
670    
671    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
672    
673            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
674              so pointers match
675    
676    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * DESCRIPTION (Date): set ready for release -- 0.999375-1
679    
680    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
681    
682            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
683              src/chm_common.c, src/chm_common.h: Change API for
684              numeric_as_chm_dense and N_AS_CHM_DN
685    
686    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
687    
688            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
689            * tests/matprod.R: regr.test for it
690    
691    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
694            * tests/group-methods.R: and regression-test it
695    
696    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
697    
698            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
699              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
700              triplet_to_sparse, documentation, use typedefs
701    
702    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * man/dpoMatrix-class.Rd: added 'corMatrix' example
705    
706            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
707            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
708            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
709    
710            * R/lsparseMatrix.R: bug fix in "all" method
711            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
712    
713            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
714            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
715                    + matrix |-> nMatrix coercion
716            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
717            * man/pMatrix-class.Rd: ditto
718    
719            * R/Matrix.R (Summary): method for non-dMatrix
720    
721            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
722            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
723                    test all Summary methods.
724    
725    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
728    
729    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
732    
733            * R/pMatrix.R (t?crossprod): methods for pMatrix
734    
735    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
736    
737            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
738    
739    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
740    
741            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
742              trying to fix a subtle bug - which has been somewhere else.
743    
744    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
745    
746            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
747              solve the bug
748    
749    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
750    
751            * src/dgCMatrix.c (compressed_to_TMatrix):
752    
753    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * src/Csparse.c (Rsparse_validate): new, to have some validity
756            checking for RsparseMatrix
757            * src/dgCMatrix.c (xRMatrix_validate): ditto
758            * src/dtCMatrix.c (tRMatrix_validate): ditto
759    
760    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
761    
762            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
763              lgRMatrix
764            * [r4568] DESCRIPTION: Prepare for bug-fix release
765            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
766              for declaration of cholmod_symmetry
767    
768    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
769    
770            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
771            release.
772    
773    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
774    
775            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
776              functions - no longer used
777            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
778              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
779              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
780              Alloca
781    
782    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
783    
784            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
785              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
786              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
787              src/t_gCMatrix_colSums.c: more R_CheckStack()s
788    
789    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
790    
791            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
792              the required amount of memory then call M_numeric_as_chm_dense.
793            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
794              (like Calloc but calling alloca)
795    
796    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
797    
798            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
799            and extended with more sophisticated 'col.names' option.
800            * NAMESPACE: export  printSparseMatrix()
801            * man/printSpMatrix.Rd: document, incl. examples
802    
803    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
804    
805            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
806              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
807              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
808    
809    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
810    
811            * DESCRIPTION (Version): 0.99875-4
812    
813            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
814            some dimnames perservation.
815    
816            * R/dsTMatrix.R (t-method): keep dimnames
817            * R/dtTMatrix.R:  ditto
818    
819            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
820            and ncol(.) < 10
821    
822            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
823            from Mutils.h
824    
825            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
826            e.g. in as(<ngCMatrix>, "matrix")
827    
828    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
829    
830            * [r4529] .: Create a branch for the API changes from the 0.99875
831              series to the 0.999375 series
832            * [r4530] DESCRIPTION, inst/include/Matrix.h,
833              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
834              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
835              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
836              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
837              as_cholmod_x functions
838    
839    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
840    
841            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
842              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
843              to Comparisons
844    
845    >>>>>>> .merge-right.r4561
846    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
847    
848            * DESCRIPTION (Version): 0.99875-3 ready to be released.
849    
850            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
851    
852            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
853            that should also work in a future version of R.
854    
855    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
858    
859            * R/sparseVector.R: more *sparseVector coercions, notably for
860            non - double ones.
861    
862    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
863    
864            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
865              notably the new ones building on the new .Call(.)s:
866    
867            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
868            all 4 of [dlin]gCMatrix_colSums().
869    
870    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
871    
872            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
873            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
874              result
875    
876    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
877    
878            * R/kronecker.R: fix typo (could lead to inf.recursion)
879            * test/simple.R: testing that
880    
881            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
882            method as well (which can have arguments, show() can't).
883    
884    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
885    
886            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
887              added dgCMatrix_colSums for [col,row][Sums,Means]
888    
889    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
890    
891            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
892              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
893              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
894            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
895              class
896            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
897              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
898              row names to store the levels - duh!  Added an example.
899    
900    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
901    
902            * src/Csparse.c (Csparse_validate): check for *repeated* entries
903            thanks to example from Christian Buchta; with a test here:
904            * tests/simple.R:
905    
906    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
907    
908            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
909            of colSums(*, sparseResult = TRUE)
910    
911    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
912    
913            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
914            'na.rm = FALSE' as "everywhere" else in R.
915    
916    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
917    
918            * [r4421] src/CSparse_install.sh: Modify for new organization of
919              CSparse package
920            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
921              SuiteSparse
922            * [r4426] src/Makefile: add ./UFconfig to the include path for
923              compilation
924            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
925            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
926              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
927    
928    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
929    
930            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
931            * R/sparseMatrix.R (prSpMatrix): now gives a message about
932            suppressed column names.
933    
934    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
935    
936            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
937              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
938              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
939              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
940              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
941              Remove warnings after change to const char* CHAR
942    
943    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
944    
945            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
946              type of M_cholmod_ssmult
947    
948    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
949    
950            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
951              src/init.c: Yet another cholmod export - cholmod_ssmult
952    
953    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
954    
955            * NAMESPACE: exported drop0(), since
956            * man/drop0.Rd: I have seen several cases, I really wanted to use
957            it, so our users may want too.
958    
959    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
960    
961            * man/colSums.Rd: separately document colSums() etc, since these
962            have the extra argument 'sparseResult'.
963    
964    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
965    
966            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
967            * man/spMatrix.Rd: docu., including examples
968    
969            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
970            in order to make colMeans() etc fast *and* correct.
971            * R/sparseVector.R (replSPvec): "[<-" functionality for
972            sparseVectors; tested in
973            * tests/simple.R:
974    
975    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
976    
977            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
978            (very) sparse Matrices; output similar to Matlab's print().
979    
980    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
981    
982            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
983            0-based, indices (Jose Quesada <quesada@gmail.com>).
984    
985    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
986    
987            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
988    
989    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
990    
991            * R/Auxiliaries.R (sparsapply): new utility, much faster than
992            tapply1() for large sparse matrices.
993    
994    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
995    
996            * R/Matrix.R (dim<-): reshape now via sparseVector.
997    
998            * R/sparseVector.R: methods and function for
999            * R/AllClass.R: new "sparseVector" class and daughters.
1000            * NAMESPACE: export new classes
1001    
1002    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1003    
1004            * DESCRIPTION (Version): 0.99875-1
1005            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1006    
1007    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1008    
1009            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1010            indexing
1011            * tests/indexing.R: test set for that.
1012    
1013    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1014    
1015            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1016            entries.
1017            * tests/indexing.R(out): add regression test for it
1018    
1019    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
1021            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1022            name for "!" method definitions.
1023    
1024    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1025    
1026            * R/Tsparse.R (intI): new utility, used for "[" :
1027                    Cleanup up there, and fixes for duplicated indices - more TODO!
1028    
1029            * tests/indexing.R(out): more tests
1030    
1031    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1032    
1033            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1034            code that is now part of the R Lapack library.
1035    
1036            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1037            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1038    
1039    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1040    
1041            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1042    
1043    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1044    
1045            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1046            up with extraneous names '0'...'<n-1>'
1047    
1048    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1049    
1050            * R/dgTMatrix.R (mat2dgT): care about NAs
1051    
1052    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1053    
1054            * R/kronecker.R: triangularity preserving methods
1055    
1056    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1057    
1058            * R/kronecker.R: new file collecting kronecker() methods in one
1059                    place.  Goal: become much faster!
1060    
1061    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1062    
1063            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1064            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1065            can be much faster.
1066    
1067            * tests/matprod.R: add regression tests for these (upper & lower).
1068    
1069    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1070    
1071            * R/Matrix.R (diff): method for our Matrices.
1072    
1073            * R/sparseMatrix.R (isDiagonal): check dim()!
1074    
1075    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1076    
1077            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1078            proposal from Tamas Papp.
1079    
1080    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1081    
1082            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1083    
1084            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1085            rather define and export  cBind() and rBind() only.
1086            --> useRs *must* change code that used to have cbind()/rbind() !!
1087    
1088            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1089            * R/bind.Rout.save: ditto
1090    
1091    2007-02-16  Douglas Bates  <bates@r-project.org>
1092    
1093            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1094            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1095            const modifier on declaration of the array 'valid'
1096    
1097    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1098    
1099            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1100    
1101    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1102    
1103            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1104    
1105            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1106            * tests/simple.R: test the above and some of these coercions:
1107    
1108            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1109                    be careful to avoid infinite recursion, using new coercions in
1110            * R/ngCMatrix.R and nsC... and ntC...
1111            * R/lsparseMatrix.R: ditto
1112    
1113            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1114    
1115            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1116            * R/Rsparse.R: reactivate .Call()s
1117    
1118            * tests/Class+Meth.R: a bit more on actual classes
1119    
1120    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1121    
1122            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1123    
1124    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1125    
1126            * DESCRIPTION (Version): 0.9975-10 to upload
1127    
1128            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1129            specific classes less unconditionally.
1130    
1131            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1132    
1133            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1134    
1135            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1136            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1137            R_to_CMatrix segfaults on one platform.
1138            Eliminate most coercion method to *specific* classes, and replace
1139            with virtual classes coercions.
1140    
1141    
1142    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1143    
1144            * src/init.c: export the CHM...._validate() placeholders, since
1145            they *are* called.
1146    
1147            * tests/Class+Meth.R (classCanCoerce): and starting to test
1148            all as(<from>, <to>)
1149    
1150    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1151    
1152            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1153            * tests/indexing.R: tested now
1154            * tests/indexing.Rout.save: updated
1155    
1156            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1157            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1158            appropriate.
1159    
1160            * NAMESPACE: export a trivial
1161            * R/Matrix.R: drop() Matrix-method
1162    
1163            * R/AllClass.R: moved all prototypes to virtual super classes.
1164    
1165            * R/Rsparse.R: many more coercions to have less exceptions in
1166            * tests/Class+Meth.R:
1167    
1168            * R/Ops.R (Compare): tweak for case with NA
1169            * tests/simpl.R: hence another 'FIXME' eliminated
1170    
1171    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1172    
1173            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1174            objects.
1175    
1176            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1177              and more of "!", "&", "|", all, any; coercions
1178    
1179            * R/Rsparse.R: many coercions (which enable quite a few other
1180            methods), thanks to enhancements in
1181            * src/dgCMatrix.c (R_to_CMatrix): new, and
1182            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1183            symmetric & triangular and ..RMatrix objects.
1184    
1185            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1186            renamed file from src/dsTMatrix.c;
1187            now dealing with symmetric and triangular Tsparse coercions, both
1188            to dense and general.
1189    
1190    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1191    
1192            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1193    
1194            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1195            where sensible when the <numeric> is of length > 1.
1196    
1197    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1198    
1199            * R/Matrix.R ([<-): for M[] <- value: fix length
1200    
1201    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1202    
1203            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1204            * R/ndenseMatrix.R: new coercions n* -> l*
1205    
1206    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1207    
1208            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1209    
1210            * R/Ops.R ("Logic"): and other "Ops", many updates
1211    
1212    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1213    
1214            * src/Mutils.h (SET_DimNames): new utility
1215    
1216            * R/Auxiliaries.R (nnzero): improved and now exported via
1217    
1218            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1219    
1220    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1221    
1222            * R/diagMatrix.R (!): fix typo.
1223    
1224    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1225    
1226            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1227                    allow to pass class definition --> speedup
1228            * R/sparseMatrix.R: apply the above
1229    
1230            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1231    
1232            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1233            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1234            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1235    
1236            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1237    
1238            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1239            and use it for "sparse*" as well, since it's faster than the
1240            as_Csparse(.) way.
1241    
1242    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1243    
1244            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1245    
1246    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1247    
1248            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1249            as method for   M[ ij ] <- v
1250            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1251    
1252            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1253            FALSE answer
1254    
1255            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1256            * tests/indexing.R: test it, and some of the above
1257    
1258    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1259    
1260            * R/Auxiliaries.R (is_duplicatedT): new utility
1261    
1262    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1263    
1264            * src/init.c (R_init_Matrix): export cholmod_scale
1265    
1266    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1267    
1268            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1269            base::as.matrix to (x, ...)
1270    
1271    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1272    
1273            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1274            file; start using "Logic", hence
1275    
1276            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1277            * NAMESPACE: import and export "Logic"
1278    
1279    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1280    
1281            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1282            only needed previously to R version 2.5.0.
1283    
1284    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1285    
1286            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1287    
1288            * R/Tsparse.R (replTmat): fix subassignment of triangular
1289            * R/Csparse.R (replCmat): ditto
1290            * tests/indexing.R: more tests, incl the above fix
1291    
1292    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1293    
1294            * R/Auxiliaries.R (drop0): extend for non CSparse
1295            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1296    
1297            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1298                    use uplo correctly (!); other places: use uplo_P() macro
1299    
1300            * R/Csparse.R (replCmat): call diagU2N() when needed
1301            * R/Tsparse.R (replTmat): ditto
1302    
1303            * src/dtCMatrix.c (tCMatrix_validate): new
1304            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1305            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1306    
1307            * R/diagMatrix.R (replDiag): to use in [<-
1308    
1309    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1310    
1311            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1312                    also more general diagU2N().
1313    
1314    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1315    
1316            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1317            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1318    
1319    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1320    
1321            * tests/bind.R: a few more cases
1322            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1323    
1324            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1325            * R/ddenseMatrix.R (cbind2/rbind2)
1326            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1327            * tests/indexing.R
1328            * tests/indexing.Rout.save: updated
1329    
1330    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1331    
1332            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1333            * tests/indexing.R
1334    
1335    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1336    
1337            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1338            align with proper position of "0", i.e., right for integers.
1339            argument 'align' by default is "fancy".
1340    
1341    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1342    
1343            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1344            * R/Csparse.R: and fix "Compare" for more cases.
1345            * tests/Class+Meth.R: test some of these (m == m, m != m)
1346    
1347    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1348    
1349            * R/lsparseMatrix.R: all() and any() methods
1350            * R/ldenseMatrix.R:      ditto
1351            * NAMESPACE, R/Matrix.R: ditto
1352    
1353            * man/all-methods.Rd: document them minimally
1354    
1355            * tests/simple.R: add a few examples for these
1356    
1357    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1358    
1359            * R/Tsparse.R ([): fix long standing typo in symmetric case
1360            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1361    
1362    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1363    
1364            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1365            to LL before converting to a sparse matrix. (The LDL form can be
1366            converted to a sparse matrix but it is implicitly a unit
1367            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1368    
1369    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1370    
1371            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1372    
1373    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1374    
1375            * DESCRIPTION (Version): updated -> release 0.9975-7
1376            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1377    
1378    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1379    
1380            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1381    
1382    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1383    
1384            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1385            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1386            is exactly singular.
1387    
1388    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1389    
1390            * DESCRIPTION (Date): updated -> release 0.9975-6
1391    
1392    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1393    
1394            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1395            now returns symmetric.
1396    
1397            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1398    
1399            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1400            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1401    
1402            * R/Auxiliaries.R (.type.kind): added
1403    
1404    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1405    
1406            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1407            running src/CSparse_install.sh
1408    
1409            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1410    
1411    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1412    
1413            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1414            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1415    
1416            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1417    
1418            * tests/Class+Meth.R (tstMatrixClass): now assure
1419            the (important in method programming) property :
1420    
1421                    ###>>  Every "Matrix" is either
1422                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1423    
1424                    (where "*" stands for "Matrix")
1425    
1426            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1427    
1428            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1429            * tests/validObj.R: checks for "comparison"
1430    
1431            * R/sparseMatrix.R ([): improved indexing for sparse;
1432                    trying to keep <symmetric>[ n, n] symmmetric
1433    
1434            * tests/indexing.R: indexing for logical sparse now ok
1435    
1436    
1437    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1438    
1439            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1440    
1441            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1442    
1443    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1444    
1445            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1446    
1447            * tests/simple.R: validObject() checking the above.
1448    
1449            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1450            replacing both dgCMatrix_validate and lgCM*.
1451    
1452            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1453            fix dimnames setting in other places.
1454            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1455    
1456    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1457    
1458            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1459    
1460            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1461            symmetry test, via
1462            * R/Auxiliaries.R (.as.dgC.0.factors):
1463    
1464    2006-11-01  Douglas Bates  <bates@r-project.org>
1465    
1466            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1467            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1468            <CsparseMatrix>) added
1469    
1470    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1471    
1472            * tests/matprod.R: add a variation of Harri's example
1473    
1474            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1475            recursive infinitely.
1476    
1477            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1478    
1479            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1480    
1481    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1482    
1483            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1484            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1485            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1486            satisfy the above test.
1487    
1488    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1489    
1490            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1491    
1492            * R/dgCMatrix.R: solve(a, b="missing") based on
1493            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1494            RHS = NULL.
1495    
1496            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1497            add more (needed) [t]crossprod() methods.
1498    
1499            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1500    
1501            * R/Auxiliaries.R (as_CspClass): cleanup
1502            (drop0): internal utility for "Csparse_drop(*, 0)"
1503            (.bail.out.2): encourage active feedback
1504    
1505    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1506    
1507            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1508    
1509            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1510            non-valid or 'sorted' case).
1511    
1512            * R/dsparseMatrix.R: add "chol" method.
1513            * R/ddenseMatrix.R: ditto
1514    
1515            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1516            * NAMESPACE (Ops)
1517            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1518            coercion; deprecating direct lower level coercions.
1519    
1520            * R/*.R (seq): use seq_len() and seq_along() where possible.
1521    
1522    
1523    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1524    
1525            * DESCRIPTION (Version): 0.9975-5 ready for release
1526    
1527    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1528    
1529            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1530    
1531    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1532    
1533            * R/AllClass.R (corMatrix): add 'validity' check;
1534                    comment out unused "LDL" class definition
1535            * NAMESPACE: mention, but do not export "LDL" class
1536            * R/corMatrix.R: new (simple), needed for R-devel with
1537            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1538              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1539    
1540    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1541    
1542            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1543            use Rprintf and R's error handling.
1544    
1545    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1546    
1547            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1548            * tests/matprod.R: add tests for the bug fixed.
1549    
1550    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1551    
1552            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1553            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1554    
1555    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1556    
1557            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1558    
1559    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1560    
1561            * DESCRIPTION (Version): 0.9975-3
1562    
1563            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1564            (sparse) matrices.
1565            * man/bdiag.Rd: docu + examples
1566    
1567            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1568    
1569            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1570            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1571    
1572            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1573            that result is sparse or diagonal (and not dense).
1574    
1575            * man/Subassign-methods.Rd: fix examples
1576    
1577            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1578            should always return a sparse (and not sometimes a diagonal) matrix.
1579    
1580    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1581    
1582            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1583    
1584    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1585    
1586            * DESCRIPTION (Version): 0.9975-2
1587    
1588            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1589    
1590    2006-10-02  Douglas Bates  <bates@R-project.org>
1591    
1592            * tests/dg_Matrix.R: Simplify test taking into account new code.
1593    
1594    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1595    
1596            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1597    
1598            * R/lsTMatrix.R: new files w/ missing methods
1599            * R/nsTMatrix.R:  "  'for completeness'
1600    
1601            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1602    
1603            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1604    
1605    
1606    2006-09-28  Douglas Bates  <bates@R-project.org>
1607    
1608            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1609            included.
1610    
1611            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1612            Export C-callable functions used in Zt_create in lme4.
1613    
1614    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1615    
1616            * DESCRIPTION (Version): 0.9975-1
1617    
1618            * tests/simple.R: less checks fail; using NA, found that our
1619                    kronecker() is not base-compatible with NA's.
1620    
1621            * R/dMatrix.R: "Compare" method now implemented for all cases
1622    
1623            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1624    
1625            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1626    
1627            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1628            * src/dspMatrix.c (dspMatrix_validate): ditto
1629    
1630            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1631              including coercion to [nl]tTMatrix.
1632    
1633            * R/diagMatrix.R (show): print a header line as for other classes.
1634    
1635    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1636    
1637            * src/Makefile.win (SUBDIRS): fix typo
1638    
1639    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1640    
1641            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1642    
1643  2006-09-18  Douglas Bates  <bates@stat.wisc.edu>  2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1644    
1645          * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x          * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
# Line 54  Line 1696 
1696          * tests/: adaptions          * tests/: adaptions
1697          * src/chm_common.c (chm_dense_to_SEXP): and others:          * src/chm_common.c (chm_dense_to_SEXP): and others:
1698                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1699          * src/Csparse.c, etc: dito          * src/Csparse.c, etc: ditto
1700    
1701  2006-09-11  Douglas Bates  <bates@R-project.org>  2006-09-11  Douglas Bates  <bates@R-project.org>
1702    
# Line 73  Line 1715 
1715          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1716    
1717          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1718          * man/tcrossprod.Rd: dito          * man/tcrossprod.Rd: ditto
1719    
1720  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1721    
# Line 116  Line 1758 
1758    
1759          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1760          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1761          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
1762          * R/Csparse.R: dito          * R/Csparse.R: ditto
1763    
1764  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1765    
# Line 133  Line 1775 
1775    
1776          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1777          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1778          (.is.diagonal): dito          (.is.diagonal): ditto
1779    
1780          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1781    

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