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revision 1682, Fri Dec 1 18:42:40 2006 UTC revision 2223, Fri Jul 18 23:04:48 2008 UTC
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1    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
4            versions.
5    
6            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
7            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
8    
9            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
10              AS_CHM_SP() which includes diagU2N.
11    
12    
13    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
14    
15            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
16              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
17              new solve method
18            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
19              Csparse_diagU2N functionality into Matrix_as_cs
20    
21    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * [r2215] inst/doc/factor2sparse.Rnw: revive a year-old unfinished
24              vignette
25            * [r2214] R/AllGeneric.R: cosmetic
26            * [r2213] man/image-methods.Rd: typo ("non-number" :-\ )
27    
28    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
29    
30            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
31              argument with default TRUE
32            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
33              Csparse_diagU2N
34            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
35              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
36              parent array; new solve method for signature(a = "dtCMatrix", b =
37              "sparseMatrix")
38    
39    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/diagMatrix.R (.bdiag): also keep triangular
42            * [r2209] ChangeLog, DESCRIPTION, R/diagMatrix.R, inst/test-tools.R,
43              man/dsCMatrix-class.Rd, man/dsyMatrix-class.Rd, tests/Simple.R:
44              bdiag() improvements of last week
45    
46    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
47    
48            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
49              messages
50    
51    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
54            symmetric- or nsparse-Matrix, also fixing the bug introduced with
55            the new version (.999375-10).
56    
57            * tests/Simple.R: regression test for the bugs.
58    
59    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/sparseVector.R (spV2M): fix for "isparseVector".
62            Further, fix <diag> -> <sparseVector> coercion
63            (repSpV): add rep(<sparseVector>, .) method
64    
65            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
66            use as.vector(.).
67    
68            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
69    
70            * R/AllClass.R: new (hidden) class union "scarceMatrix"
71            * R/AllClass.R: sparseVector: add prototype
72    
73            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
74            Kasper Kristensen
75    
76    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * tests/other-pkgs.R: add more interesting Matrix -> graph
79    
80    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
83            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
84    
85    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * DESCRIPTION: release 0.999375-10 to CRAN
88    
89            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
90            .bdiag().
91            * man/bdiag.Rd: update, including test.
92    
93    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * tests/Simple.R: add minimal bdiag() checks
96    
97            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
98              factor out the Tsparse - internal computation into new .bdiag()
99    
100    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/nsparseMatrix.R: specific fast all() and any() methods.
103    
104            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
105            when trying to produce too large result.
106    
107            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
108            very large matrices.
109    
110            * R/sparseMatrix.R (printSpMatrix2): new function, used by
111            show(<sparseMatrix>).
112    
113            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
114    
115    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * src/Mutils.c (m_encodeInd, m_encodeInd2):
118            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
119    
120            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
121            big matrices): -> 2nd argument 'di' instead of 'nr' !
122    
123    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/dtCMatrix.R: faster dgC* -> dtC* method
126            * tests/Simple.R: (hence removed "FIXME")
127    
128            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
129            which can be be turned off for possible speed gains.
130    
131    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
134    
135            * R/not.R: fix !<ldiMatrix>
136            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
137    
138            * R/diagMatrix.R (Ops): fix one-off thinko in
139            <diagonal> o <numeric> methods
140    
141            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
142    
143    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
146            * tests/Simple.R: testing the above
147    
148    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
151    
152    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
155            * NAMESPACE (unname): finally exported
156    
157    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/Auxiliaries.R (cholMat): possibly keep packed
160    
161            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
162            for R < 2.7.0.
163    
164            * R/Tsparse.R ([): for triangularMatrix, check if result may be
165            triangular.
166            * tests/indexing.R: regression test
167    
168    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
171            * R/Ops.R: more methods, for lMatrix/nMatrix
172    
173    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/expm.R: new file for all expm() methods; notably new ones for
176            diagonal*, triangular*, symmetric* and also simple "matrix".
177    
178    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
181    
182            * inst/test-tools.R (assert.EQ.mat): better message when not equal
183    
184            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
185    
186            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
187            [dl]denseMatrix {identical slots; but more logical method dispatch}
188    
189    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
192    
193            * R/diagMatrix.R (determinant): method
194    
195    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
198    
199            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
200    
201            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
202            its diagonal
203    
204    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
207    
208            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
209    
210            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
211    
212            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
213    
214    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
217    
218            * R/Ops.R (.do.Logic.lsparse): fix NA case
219    
220            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
221    
222            * R/Auxiliaries.R (nnzero): fix special cases, using
223            * R/Auxiliaries.R (indDiag): new utility
224            * R/Auxiliaries.R (indTri): new argument 'diag'
225    
226            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
227    
228    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
231    
232            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
233            ".tCMatrix" triangular matrix.
234    
235            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
236            'clx' can be class *or* class representation.
237            (nnzSparse): new.
238            (non0ind): new 'xtendSymm' argument; used in
239            * R/Ops.R:
240    
241            * R/pMatrix.R: more efficient determinant() method
242    
243    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
246            * [disactivated] NAMESPACE: export(det)
247    
248            * R/diagMatrix.R (mkDiag): new substitute for diag()
249    
250            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
251            (as0, as1): new utility.
252    
253            * R/Csparse.R (diag, band): need diagU2N()
254    
255            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
256    
257            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
258    
259            * R/Ops.R (Compare): fix <nsp> o <nsp> case
260    
261            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
262    
263    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/Auxiliaries.R (signPerm): new utility for
266            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
267    
268            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
269            since we have our own error handler (and can use tryCatch() from R).
270    
271    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
274    
275            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
276            when not positive definite.
277    
278            * R/Auxiliaries.R (asTri): new auxiliary
279            (non0.i): make *much* faster for Tsparse with many non-zero
280            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
281    
282            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
283            test-tools.R , see below
284    
285            * R/dMatrix.R: fix "Summary" method: + diagU2N()
286    
287            * NAMESPACE, R/Matrix.R: add mean() method
288    
289    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
292            cold-hot colors; try *changed* default useAbs = FALSE
293            * man/image-methods.Rd:  nice examples
294    
295    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * inst/test-tools.R (checkMatrix): new function for modularizing part
298            of tstMatrixClass() in tests/Class+Meth.R
299    
300            * R/dsCMatrix.R: coercion from "matrix"
301            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
302    
303            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
304            add test for as(matrix(,0,0), <class>)
305    
306    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
309            work as determinant(matrix(,0,0)).
310    
311            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
312            * man/sparseLU-class.Rd: ditto
313    
314            * R/dgCMatrix.R (determinant): method building on lu()
315            * R/sparseMatrix.R, Matrix.R, ...: ditto
316    
317            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
318    
319    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
322            pattern matrices.
323    
324    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * src/dense.c (dense_to_Csparse): all declarations *before*
327            R_CheckStack(); needed e.g. for ancient gcc 2.96.
328    
329    
330    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * DESCRIPTION (Version): 0.999375-9 --- need to release
333            for R-devel (and R 2.7.0 alpha soon).
334    
335            * R/AllClass.R: drop "double" from "atomicVector" class union
336    
337            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
338            * R/dgeMatrix.R: ditto
339    
340            * R/sparseMatrix.R (summary): count NAs
341    
342            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
343    
344    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
347            order to become compatible to new R 2.7.0 base::rcond().
348    
349    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
352    
353            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
354    
355            * inst/test-tools.R (isValid): new utility, used much in
356            * tests/simple.R:
357    
358            * man/BunchKaufman-methods.Rd: added too
359    
360    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * R/dsyMatrix.R: add BunchKaufman() methods.
363            * R/dspMatrix.R:
364    
365            * src/init.c: add dsyMatrix_trf
366    
367    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
368    
369            * DESCRIPTION (Version): release 0.999375-7
370            * src/CHMfactor.c (CHMfactor_update): fix
371    
372    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
375            internal_chm_factor().
376    
377            * R/AllGeneric.R: do *not* define a "chol" generic
378                    (but rather use the implicit one *without* making pivot
379                    part of the signature)
380            * R/*.R: drop the 'pivot' from chol's signature and make
381                    'pivot=FALSE' a default argument of method definitions.
382    
383            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
384            version of Matrix
385    
386    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
389    
390            * R/sparseMatrix.R (is.na): new simple method
391            * R/denseMatrix.R (is.na): ditto.
392    
393            * R/diagMatrix.R (.symDiagonal): newly exported utility.
394    
395            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
396    
397            * src/UFsparse_download.sh: -->
398            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
399    
400    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
403            functionality; barely tested in
404            * tests/factorizing.R
405    
406            * src/Csparse.c (diag_tC): new functionality to enable faster
407            determinant(<dsCMatrix>, .) in
408            * R/dsCMatrix.R
409    
410    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
411    
412            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
413              src/CHMfactor.c, src/CHMfactor.h,
414              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
415              Log-determinant of the parent matrix from a CHMfactor object as
416              chm_factor_ldetL2; documentation and support
417    
418    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
421    
422    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
425            warning.
426    
427    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
430    
431            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
432              <diagonal> o <sparse_triangular>
433              setAs(., "nMatrix") added.
434    
435            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
436    
437            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
438                    new argument 'checkDense = FALSE'.
439    
440    
441    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
444            back-permutation of the matrix exponential.
445    
446            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
447    
448            * DESCRIPTION (Date,Version): ready to release 0.999375-5
449    
450            * tests/simple.R: testing diagN2U
451    
452    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * R/Auxiliaries.R (diagN2U): interface to
455    
456            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
457    
458            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
459    
460    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * src/chm_common.c (chm_diagN2U): new utility.
463    
464            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
465            make use of chm_diagN2U() and hence now preserve triangularity and
466            unit-triangularity.
467    
468            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
469    
470    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
473    
474            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
475            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
476    
477            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
478    
479            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
480    
481            * src/chm_common.c (AS_CHM_FINISH): add note about problem
482            for triangular (diag = "U").
483    
484    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
486            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
487            * R/bind.R:  .Call(dense_to_Csparse, *)
488    
489    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
490    
491            * R/Matrix.R (Matrix): no longer use coercions to specific classes
492                    (since we are discouraging them in user code).
493    
494            * tests/*.R: also replaces coercions to specific classes by
495            coercions to super classes.
496    
497            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
498    
499    
500    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
503    
504            * src/dense.c (dense_band): generalized from ddense_band
505    
506            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
507              now for "denseMatrix" (instead of just "ddense*"); much
508              simplified setMethod()s for these.
509    
510            * src/dense.c (dense_to_symmetric): generalized from ddense_*
511    
512    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
515            version of as(*, "symmetricMatric").
516    
517            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
518            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
519    
520    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * R/Matrix.R (subset.ij): utility, as first step to faster
523               M [ <ij-matrix> ] indexing.
524    
525            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
526    
527            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
528            for more efficient symmpart() and skewpart() methods.
529    
530            * src/Mutils.c (equal_string_vectors): utility
531    
532            * src/dense.c (ddense_to_symmetric): new function used in
533    
534            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
535    
536            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
537            order to match the generic (and evade .local(..)).
538    
539            * R/dsCMatrix.R: dgC -> dsC: use C code!
540    
541            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
542            as per TODO
543    
544            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
545    
546            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
547    
548    
549    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
552    
553            * R/Auxiliaries.R (non0.i): take out of non0ind
554    
555            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
556            make tril(), triu(), band() work for "matrix" and all "dense*"
557    
558            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
559            * tests/simple.R: test the fix above
560    
561            * R/sparseMatrix.R ([): simplification: no coerce to <general>
562                    before we use as(., <Tsparse>)[...] anyway
563    
564            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
565    
566            * R/triangularMatrix.R (isTriangular): methods for all subclasses
567            instead of "triangularMatrix" -- just to disambiguate
568    
569    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
572            * tests/indexing.R: example that fails above
573    
574    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
577            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
578                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
579    
580            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
581            * src/Tsparse.h, init.c: ditto
582            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
583                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
584            * R/sparseMatrix.R (isTriangular): hence simplified
585    
586    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
587    
588            * R/Ops.R (.Arith.Csparse): new utility factored out of former
589              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
590    
591    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
594    
595            * inst/test-tools.R (isOrthogonal): new function; also file restructured
596    
597    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
600            coercion to "nMatrix" and "pMatrix"
601    
602            * R/AllClass.R: "Schur" class;  "number" class union
603            * man/number-class.Rd:
604            * man/Schur-class.Rd:
605    
606            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
607            (.simpleSchur): Schur() method for diagonal matrices
608            (.triSchur):    Schur() method for triangular matrices
609            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
610    
611    
612    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
615    
616    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
617    
618            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
619                    in order to ensure 'system = *' is not lost;
620                    formals()$system instead of cut&paste.
621            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
622    
623    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
624    
625            * DESCRIPTION (Date): make ready for release --> 0.999375-4
626    
627            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
628    
629    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
632                    and hence does as.vector(.).
633            * man/pMatrix-class.Rd: docs
634            * R/sparseMatrix.R: fix for printing "integer sparse"
635    
636            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
637    
638            * R/Matrix.R and others: use "exact" function argument list for
639                    both "["   : (x, i,j, ..., drop)
640                    and  "[<-" : (x, i,j, ..., value)
641    
642            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
643            * R/Tsparse.R (replTmat):    ditto
644            * R/diagMatrix.R (replDiag): ditto
645            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
646            * tests/indexing.R: testing the above
647    
648    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
649    
650            * R/sparseMatrix.R (cov2cor): method for sparse matrices
651    
652            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
653    
654            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
655    
656            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
657    
658    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
659    
660            * R/Matrix.R: "generic" cov2cor() method
661    
662            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
663                    speed up Q %*% D %*% t(Q)
664            * tests/dpoMatrix.R: test nearPD()
665    
666    2007-12-05  Doug Bates and Martin Maechler
667    
668            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
669            stats::xtabs() allowing to create sparse matrices.
670    
671    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
674    
675    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
676    
677            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
678    
679    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
680    
681            * R/LU.R: solve() method for "denseLU"
682    
683    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * DESCRIPTION (Version): 0.999375-3 preparing for release
686    
687            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
688    
689            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
690    
691    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
694              thanks to Kasper Kristensen.
695            * tests/matprod.R: regression test for that.
696    
697    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
698    
699            * [r4778] R/AllGeneric.R: Check R version before defining generics for
700              primitives
701    
702    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/denseMatrix.R (rcond): method
705            * R/sparseQR.R (rcond): method, use x or t(x)
706    
707    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
708    
709            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
710            matrices.
711            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
712    
713            * man/rcond.Rd: mention the more general definition, and add
714            example for non-square matrices.
715    
716            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
717    
718    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
721    
722    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
725            * tests/indexing.R: add new regression for the above cases.
726    
727    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * src/Mutils.h (__sun): clause for alloca.h on Solaris
730    
731    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
732    
733            * DESCRIPTION (Date, Version): 0.999375-2
734    
735    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737            * R/HBMM.R (readMM): make work for pattern matrices as well
738    
739    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
740    
741            * [r4730] src/Mutils.h: declare alloca
742            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
743              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
744              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
745              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
746              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
747              methods; switch writeMM to use CHOLMOD code; repair readMM
748    
749    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
750    
751            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
752            Oehlschlaegel's ... result type still to be discussed!
753    
754    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
755    
756            * man/image-methods.Rd: new, combining all image() methods
757    
758    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
761            to work via dgC...
762    
763            * R/Matrix.R (Matrix): special treatment for "table" (S3)
764    
765    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * R/dgTMatrix.R (image): change defaults to
768                    aspect = "iso", colorkey = FALSE
769    
770    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
771    
772            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
773            must copy its *expanded* x slot before LAPACK call.
774    
775            * tests/matprod.R: test the last days' changes.
776    
777    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
778    
779            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
780              as well as in sources
781            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
782              Lapack call
783    
784    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
785    
786            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
787                    ("Matrix", "matrix") which is needed in some cases.
788            Ditto for solve().
789    
790            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
791            infinite recursion in dispatch for some cases.
792    
793    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
794    
795            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
796              so pointers match
797    
798    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
799    
800            * DESCRIPTION (Date): set ready for release -- 0.999375-1
801    
802    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
803    
804            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
805              src/chm_common.c, src/chm_common.h: Change API for
806              numeric_as_chm_dense and N_AS_CHM_DN
807    
808    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
809    
810            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
811            * tests/matprod.R: regr.test for it
812    
813    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
814    
815            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
816            * tests/group-methods.R: and regression-test it
817    
818    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
819    
820            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
821              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
822              triplet_to_sparse, documentation, use typedefs
823    
824    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
825    
826            * man/dpoMatrix-class.Rd: added 'corMatrix' example
827    
828            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
829            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
830            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
831    
832            * R/lsparseMatrix.R: bug fix in "all" method
833            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
834    
835            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
836            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
837                    + matrix |-> nMatrix coercion
838            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
839            * man/pMatrix-class.Rd: ditto
840    
841            * R/Matrix.R (Summary): method for non-dMatrix
842    
843            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
844            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
845                    test all Summary methods.
846    
847    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
848    
849            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
850    
851    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
852    
853            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
854    
855            * R/pMatrix.R (t?crossprod): methods for pMatrix
856    
857    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
858    
859            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
860    
861    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
862    
863            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
864              trying to fix a subtle bug - which has been somewhere else.
865    
866    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
867    
868            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
869              solve the bug
870    
871    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
872    
873            * src/dgCMatrix.c (compressed_to_TMatrix):
874    
875    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
876    
877            * src/Csparse.c (Rsparse_validate): new, to have some validity
878            checking for RsparseMatrix
879            * src/dgCMatrix.c (xRMatrix_validate): ditto
880            * src/dtCMatrix.c (tRMatrix_validate): ditto
881    
882    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
883    
884            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
885              lgRMatrix
886            * [r4568] DESCRIPTION: Prepare for bug-fix release
887            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
888              for declaration of cholmod_symmetry
889    
890    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
891    
892            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
893            release.
894    
895    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
896    
897            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
898              functions - no longer used
899            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
900              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
901              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
902              Alloca
903    
904    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
905    
906            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
907              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
908              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
909              src/t_gCMatrix_colSums.c: more R_CheckStack()s
910    
911    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
912    
913            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
914              the required amount of memory then call M_numeric_as_chm_dense.
915            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
916              (like Calloc but calling alloca)
917    
918    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
919    
920            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
921            and extended with more sophisticated 'col.names' option.
922            * NAMESPACE: export  printSparseMatrix()
923            * man/printSpMatrix.Rd: document, incl. examples
924    
925    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
926    
927            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
928              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
929              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
930    
931    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
932    
933            * DESCRIPTION (Version): 0.99875-4
934    
935            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
936            some dimnames perservation.
937    
938            * R/dsTMatrix.R (t-method): keep dimnames
939            * R/dtTMatrix.R:  ditto
940    
941            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
942            and ncol(.) < 10
943    
944            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
945            from Mutils.h
946    
947            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
948            e.g. in as(<ngCMatrix>, "matrix")
949    
950    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
951    
952            * [r4529] .: Create a branch for the API changes from the 0.99875
953              series to the 0.999375 series
954            * [r4530] DESCRIPTION, inst/include/Matrix.h,
955              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
956              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
957              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
958              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
959              as_cholmod_x functions
960    
961    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
962    
963            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
964              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
965              to Comparisons
966    
967    >>>>>>> .merge-right.r4561
968    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
969    
970            * DESCRIPTION (Version): 0.99875-3 ready to be released.
971    
972            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
973    
974            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
975            that should also work in a future version of R.
976    
977    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
978    
979            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
980    
981            * R/sparseVector.R: more *sparseVector coercions, notably for
982            non - double ones.
983    
984    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
985    
986            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
987              notably the new ones building on the new .Call(.)s:
988    
989            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
990            all 4 of [dlin]gCMatrix_colSums().
991    
992    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
993    
994            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
995            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
996              result
997    
998    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
999    
1000            * R/kronecker.R: fix typo (could lead to inf.recursion)
1001            * test/simple.R: testing that
1002    
1003            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
1004            method as well (which can have arguments, show() can't).
1005    
1006    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
1007    
1008            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
1009              added dgCMatrix_colSums for [col,row][Sums,Means]
1010    
1011    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
1012    
1013            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
1014              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
1015              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
1016            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
1017              class
1018            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
1019              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
1020              row names to store the levels - duh!  Added an example.
1021    
1022    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1023    
1024            * src/Csparse.c (Csparse_validate): check for *repeated* entries
1025            thanks to example from Christian Buchta; with a test here:
1026            * tests/simple.R:
1027    
1028    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1029    
1030            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
1031            of colSums(*, sparseResult = TRUE)
1032    
1033    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1034    
1035            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
1036            'na.rm = FALSE' as "everywhere" else in R.
1037    
1038    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
1039    
1040            * [r4421] src/CSparse_install.sh: Modify for new organization of
1041              CSparse package
1042            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
1043              SuiteSparse
1044            * [r4426] src/Makefile: add ./UFconfig to the include path for
1045              compilation
1046            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
1047            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
1048              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
1049    
1050    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1051    
1052            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
1053            * R/sparseMatrix.R (prSpMatrix): now gives a message about
1054            suppressed column names.
1055    
1056    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
1057    
1058            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
1059              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
1060              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
1061              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
1062              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
1063              Remove warnings after change to const char* CHAR
1064    
1065    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
1066    
1067            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
1068              type of M_cholmod_ssmult
1069    
1070    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
1071    
1072            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
1073              src/init.c: Yet another cholmod export - cholmod_ssmult
1074    
1075    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1076    
1077            * NAMESPACE: exported drop0(), since
1078            * man/drop0.Rd: I have seen several cases, I really wanted to use
1079            it, so our users may want too.
1080    
1081    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1082    
1083            * man/colSums.Rd: separately document colSums() etc, since these
1084            have the extra argument 'sparseResult'.
1085    
1086    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1087    
1088            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
1089            * man/spMatrix.Rd: docu., including examples
1090    
1091            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
1092            in order to make colMeans() etc fast *and* correct.
1093            * R/sparseVector.R (replSPvec): "[<-" functionality for
1094            sparseVectors; tested in
1095            * tests/simple.R:
1096    
1097    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1098    
1099            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1100            (very) sparse Matrices; output similar to Matlab's print().
1101    
1102    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
1103    
1104            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
1105            0-based, indices (Jose Quesada <quesada@gmail.com>).
1106    
1107    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
1108    
1109            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
1110    
1111    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1112    
1113            * R/Auxiliaries.R (sparsapply): new utility, much faster than
1114            tapply1() for large sparse matrices.
1115    
1116    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1117    
1118            * R/Matrix.R (dim<-): reshape now via sparseVector.
1119    
1120            * R/sparseVector.R: methods and function for
1121            * R/AllClass.R: new "sparseVector" class and daughters.
1122            * NAMESPACE: export new classes
1123    
1124    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1125    
1126            * DESCRIPTION (Version): 0.99875-1
1127            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1128    
1129    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1130    
1131            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1132            indexing
1133            * tests/indexing.R: test set for that.
1134    
1135    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1136    
1137            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1138            entries.
1139            * tests/indexing.R(out): add regression test for it
1140    
1141    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1142    
1143            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1144            name for "!" method definitions.
1145    
1146    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1147    
1148            * R/Tsparse.R (intI): new utility, used for "[" :
1149                    Cleanup up there, and fixes for duplicated indices - more TODO!
1150    
1151            * tests/indexing.R(out): more tests
1152    
1153    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1154    
1155            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1156            code that is now part of the R Lapack library.
1157    
1158            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1159            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1160    
1161    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1162    
1163            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1164    
1165    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1166    
1167            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1168            up with extraneous names '0'...'<n-1>'
1169    
1170    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1171    
1172            * R/dgTMatrix.R (mat2dgT): care about NAs
1173    
1174    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1175    
1176            * R/kronecker.R: triangularity preserving methods
1177    
1178    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1179    
1180            * R/kronecker.R: new file collecting kronecker() methods in one
1181                    place.  Goal: become much faster!
1182    
1183    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1184    
1185            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1186            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1187            can be much faster.
1188    
1189            * tests/matprod.R: add regression tests for these (upper & lower).
1190    
1191    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1192    
1193            * R/Matrix.R (diff): method for our Matrices.
1194    
1195            * R/sparseMatrix.R (isDiagonal): check dim()!
1196    
1197    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1198    
1199            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1200            proposal from Tamas Papp.
1201    
1202    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1203    
1204            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1205    
1206            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1207            rather define and export  cBind() and rBind() only.
1208            --> useRs *must* change code that used to have cbind()/rbind() !!
1209    
1210            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1211            * R/bind.Rout.save: ditto
1212    
1213    2007-02-16  Douglas Bates  <bates@r-project.org>
1214    
1215            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1216            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1217            const modifier on declaration of the array 'valid'
1218    
1219    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1220    
1221            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1222    
1223    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1224    
1225            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1226    
1227            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1228            * tests/simple.R: test the above and some of these coercions:
1229    
1230            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1231                    be careful to avoid infinite recursion, using new coercions in
1232            * R/ngCMatrix.R and nsC... and ntC...
1233            * R/lsparseMatrix.R: ditto
1234    
1235            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1236    
1237            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1238            * R/Rsparse.R: reactivate .Call()s
1239    
1240            * tests/Class+Meth.R: a bit more on actual classes
1241    
1242    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1243    
1244            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1245    
1246    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1247    
1248            * DESCRIPTION (Version): 0.9975-10 to upload
1249    
1250            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1251            specific classes less unconditionally.
1252    
1253            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1254    
1255            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1256    
1257            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1258            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1259            R_to_CMatrix segfaults on one platform.
1260            Eliminate most coercion method to *specific* classes, and replace
1261            with virtual classes coercions.
1262    
1263    
1264    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1265    
1266            * src/init.c: export the CHM...._validate() placeholders, since
1267            they *are* called.
1268    
1269            * tests/Class+Meth.R (classCanCoerce): and starting to test
1270            all as(<from>, <to>)
1271    
1272    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1273    
1274            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1275            * tests/indexing.R: tested now
1276            * tests/indexing.Rout.save: updated
1277    
1278            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1279            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1280            appropriate.
1281    
1282            * NAMESPACE: export a trivial
1283            * R/Matrix.R: drop() Matrix-method
1284    
1285            * R/AllClass.R: moved all prototypes to virtual super classes.
1286    
1287            * R/Rsparse.R: many more coercions to have less exceptions in
1288            * tests/Class+Meth.R:
1289    
1290            * R/Ops.R (Compare): tweak for case with NA
1291            * tests/simpl.R: hence another 'FIXME' eliminated
1292    
1293    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1294    
1295            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1296            objects.
1297    
1298            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1299              and more of "!", "&", "|", all, any; coercions
1300    
1301            * R/Rsparse.R: many coercions (which enable quite a few other
1302            methods), thanks to enhancements in
1303            * src/dgCMatrix.c (R_to_CMatrix): new, and
1304            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1305            symmetric & triangular and ..RMatrix objects.
1306    
1307            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1308            renamed file from src/dsTMatrix.c;
1309            now dealing with symmetric and triangular Tsparse coercions, both
1310            to dense and general.
1311    
1312    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1313    
1314            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1315    
1316            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1317            where sensible when the <numeric> is of length > 1.
1318    
1319    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1320    
1321            * R/Matrix.R ([<-): for M[] <- value: fix length
1322    
1323    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1324    
1325            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1326            * R/ndenseMatrix.R: new coercions n* -> l*
1327    
1328    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1329    
1330            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1331    
1332            * R/Ops.R ("Logic"): and other "Ops", many updates
1333    
1334    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1335    
1336            * src/Mutils.h (SET_DimNames): new utility
1337    
1338            * R/Auxiliaries.R (nnzero): improved and now exported via
1339    
1340            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1341    
1342    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1343    
1344            * R/diagMatrix.R (!): fix typo.
1345    
1346    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1347    
1348            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1349                    allow to pass class definition --> speedup
1350            * R/sparseMatrix.R: apply the above
1351    
1352            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1353    
1354            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1355            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1356            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1357    
1358            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1359    
1360            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1361            and use it for "sparse*" as well, since it's faster than the
1362            as_Csparse(.) way.
1363    
1364    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1365    
1366            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1367    
1368    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1369    
1370            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1371            as method for   M[ ij ] <- v
1372            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1373    
1374            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1375            FALSE answer
1376    
1377            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1378            * tests/indexing.R: test it, and some of the above
1379    
1380    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1381    
1382            * R/Auxiliaries.R (is_duplicatedT): new utility
1383    
1384    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1385    
1386            * src/init.c (R_init_Matrix): export cholmod_scale
1387    
1388    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1389    
1390            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1391            base::as.matrix to (x, ...)
1392    
1393    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1394    
1395            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1396            file; start using "Logic", hence
1397    
1398            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1399            * NAMESPACE: import and export "Logic"
1400    
1401    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1402    
1403            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1404            only needed previously to R version 2.5.0.
1405    
1406    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1407    
1408            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1409    
1410            * R/Tsparse.R (replTmat): fix subassignment of triangular
1411            * R/Csparse.R (replCmat): ditto
1412            * tests/indexing.R: more tests, incl the above fix
1413    
1414    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1415    
1416            * R/Auxiliaries.R (drop0): extend for non CSparse
1417            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1418    
1419            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1420                    use uplo correctly (!); other places: use uplo_P() macro
1421    
1422            * R/Csparse.R (replCmat): call diagU2N() when needed
1423            * R/Tsparse.R (replTmat): ditto
1424    
1425            * src/dtCMatrix.c (tCMatrix_validate): new
1426            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1427            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1428    
1429            * R/diagMatrix.R (replDiag): to use in [<-
1430    
1431    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1432    
1433            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1434                    also more general diagU2N().
1435    
1436    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1437    
1438            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1439            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1440    
1441    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1442    
1443            * tests/bind.R: a few more cases
1444            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1445    
1446            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1447            * R/ddenseMatrix.R (cbind2/rbind2)
1448            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1449            * tests/indexing.R
1450            * tests/indexing.Rout.save: updated
1451    
1452    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1453    
1454            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1455            * tests/indexing.R
1456    
1457    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1458    
1459            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1460            align with proper position of "0", i.e., right for integers.
1461            argument 'align' by default is "fancy".
1462    
1463    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1464    
1465            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1466            * R/Csparse.R: and fix "Compare" for more cases.
1467            * tests/Class+Meth.R: test some of these (m == m, m != m)
1468    
1469    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1470    
1471            * R/lsparseMatrix.R: all() and any() methods
1472            * R/ldenseMatrix.R:      ditto
1473            * NAMESPACE, R/Matrix.R: ditto
1474    
1475            * man/all-methods.Rd: document them minimally
1476    
1477            * tests/simple.R: add a few examples for these
1478    
1479    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1480    
1481            * R/Tsparse.R ([): fix long standing typo in symmetric case
1482            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1483    
1484    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1485    
1486            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1487            to LL before converting to a sparse matrix. (The LDL form can be
1488            converted to a sparse matrix but it is implicitly a unit
1489            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1490    
1491    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1492    
1493            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1494    
1495    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1496    
1497            * DESCRIPTION (Version): updated -> release 0.9975-7
1498            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1499    
1500  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1501    
1502          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method

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