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revision 1682, Fri Dec 1 18:42:40 2006 UTC revision 2183, Thu Apr 24 10:58:51 2008 UTC
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1    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/expm.R: new file for all expm() methods; notably new ones for
4            diagonal*, triangular*, symmetric* and also simple "matrix".
5    
6    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
9    
10            * inst/test-tools.R (assert.EQ.mat): better message when not equal
11    
12            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
13    
14            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
15            [dl]denseMatrix {identical slots; but more logical method dispatch}
16    
17    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
20    
21            * R/diagMatrix.R (determinant): method
22    
23    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
26    
27            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
28    
29            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
30            its diagonal
31    
32    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
35    
36            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
37    
38            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
39    
40            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
41    
42    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
45    
46            * R/Ops.R (.do.Logic.lsparse): fix NA case
47    
48            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
49    
50            * R/Auxiliaries.R (nnzero): fix special cases, using
51            * R/Auxiliaries.R (indDiag): new utility
52            * R/Auxiliaries.R (indTri): new argument 'diag'
53    
54            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
55    
56    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
59    
60            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
61            ".tCMatrix" triangular matrix.
62    
63            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
64            'clx' can be class *or* class representation.
65            (nnzSparse): new.
66            (non0ind): new 'xtendSymm' argument; used in
67            * R/Ops.R:
68    
69            * R/pMatrix.R: more efficient determinant() method
70    
71    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
74            * [disactivated] NAMESPACE: export(det)
75    
76            * R/diagMatrix.R (mkDiag): new substitute for diag()
77    
78            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
79            (as0, as1): new utility.
80    
81            * R/Csparse.R (diag, band): need diagU2N()
82    
83            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
84    
85            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
86    
87            * R/Ops.R (Compare): fix <nsp> o <nsp> case
88    
89            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
90    
91    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Auxiliaries.R (signPerm): new utility for
94            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
95    
96            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
97            since we have our own error handler (and can use tryCatch() from R).
98    
99    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
102    
103            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
104            when not positive definite.
105    
106            * R/Auxiliaries.R (asTri): new auxiliary
107            (non0.i): make *much* faster for Tsparse with many non-zero
108            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
109    
110            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
111            test-tools.R , see below
112    
113            * R/dMatrix.R: fix "Summary" method: + diagU2N()
114    
115            * NAMESPACE, R/Matrix.R: add mean() method
116    
117    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
120            cold-hot colors; try *changed* default useAbs = FALSE
121            * man/image-methods.Rd:  nice examples
122    
123    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * inst/test-tools.R (checkMatrix): new function for modularizing part
126            of tstMatrixClass() in tests/Class+Meth.R
127    
128            * R/dsCMatrix.R: coercion from "matrix"
129            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
130    
131            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
132            add test for as(matrix(,0,0), <class>)
133    
134    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
137            work as determinant(matrix(,0,0)).
138    
139            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
140            * man/sparseLU-class.Rd: ditto
141    
142            * R/dgCMatrix.R (determinant): method building on lu()
143            * R/sparseMatrix.R, Matrix.R, ...: ditto
144    
145            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
146    
147    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
150            pattern matrices.
151    
152    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * src/dense.c (dense_to_Csparse): all declarations *before*
155            R_CheckStack(); needed e.g. for ancient gcc 2.96.
156    
157    
158    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * DESCRIPTION (Version): 0.999375-9 --- need to release
161            for R-devel (and R 2.7.0 alpha soon).
162    
163            * R/AllClass.R: drop "double" from "atomicVector" class union
164    
165            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
166            * R/dgeMatrix.R: ditto
167    
168            * R/sparseMatrix.R (summary): count NAs
169    
170            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
171    
172    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
175            order to become compatible to new R 2.7.0 base::rcond().
176    
177    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
180    
181            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
182    
183            * inst/test-tools.R (isValid): new utility, used much in
184            * tests/simple.R:
185    
186            * man/BunchKaufman-methods.Rd: added too
187    
188    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/dsyMatrix.R: add BunchKaufman() methods.
191            * R/dspMatrix.R:
192    
193            * src/init.c: add dsyMatrix_trf
194    
195    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
196    
197            * DESCRIPTION (Version): release 0.999375-7
198            * src/CHMfactor.c (CHMfactor_update): fix
199    
200    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
203            internal_chm_factor().
204    
205            * R/AllGeneric.R: do *not* define a "chol" generic
206                    (but rather use the implicit one *without* making pivot
207                    part of the signature)
208            * R/*.R: drop the 'pivot' from chol's signature and make
209                    'pivot=FALSE' a default argument of method definitions.
210    
211            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
212            version of Matrix
213    
214    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
217    
218            * R/sparseMatrix.R (is.na): new simple method
219            * R/denseMatrix.R (is.na): ditto.
220    
221            * R/diagMatrix.R (.symDiagonal): newly exported utility.
222    
223            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
224    
225            * src/UFsparse_download.sh: -->
226            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
227    
228    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
231            functionality; barely tested in
232            * tests/factorizing.R
233    
234            * src/Csparse.c (diag_tC): new functionality to enable faster
235            determinant(<dsCMatrix>, .) in
236            * R/dsCMatrix.R
237    
238    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
239    
240            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
241              src/CHMfactor.c, src/CHMfactor.h,
242              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
243              Log-determinant of the parent matrix from a CHMfactor object as
244              chm_factor_ldetL2; documentation and support
245    
246    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
249    
250    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
253            warning.
254    
255    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
258    
259            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
260              <diagonal> o <sparse_triangular>
261              setAs(., "nMatrix") added.
262    
263            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
264    
265            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
266                    new argument 'checkDense = FALSE'.
267    
268    
269    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
272            back-permutation of the matrix exponential.
273    
274            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
275    
276            * DESCRIPTION (Date,Version): ready to release 0.999375-5
277    
278            * tests/simple.R: testing diagN2U
279    
280    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/Auxiliaries.R (diagN2U): interface to
283    
284            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
285    
286            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
287    
288    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * src/chm_common.c (chm_diagN2U): new utility.
291    
292            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
293            make use of chm_diagN2U() and hence now preserve triangularity and
294            unit-triangularity.
295    
296            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
297    
298    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
301    
302            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
303            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
304    
305            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
306    
307            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
308    
309            * src/chm_common.c (AS_CHM_FINISH): add note about problem
310            for triangular (diag = "U").
311    
312    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
315            * R/bind.R:  .Call(dense_to_Csparse, *)
316    
317    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/Matrix.R (Matrix): no longer use coercions to specific classes
320                    (since we are discouraging them in user code).
321    
322            * tests/*.R: also replaces coercions to specific classes by
323            coercions to super classes.
324    
325            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
326    
327    
328    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
331    
332            * src/dense.c (dense_band): generalized from ddense_band
333    
334            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
335              now for "denseMatrix" (instead of just "ddense*"); much
336              simplified setMethod()s for these.
337    
338            * src/dense.c (dense_to_symmetric): generalized from ddense_*
339    
340    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
343            version of as(*, "symmetricMatric").
344    
345            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
346            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
347    
348    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/Matrix.R (subset.ij): utility, as first step to faster
351               M [ <ij-matrix> ] indexing.
352    
353            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
354    
355            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
356            for more efficient symmpart() and skewpart() methods.
357    
358            * src/Mutils.c (equal_string_vectors): utility
359    
360            * src/dense.c (ddense_to_symmetric): new function used in
361    
362            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
363    
364            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
365            order to match the generic (and evade .local(..)).
366    
367            * R/dsCMatrix.R: dgC -> dsC: use C code!
368    
369            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
370            as per TODO
371    
372            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
373    
374            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
375    
376    
377    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
380    
381            * R/Auxiliaries.R (non0.i): take out of non0ind
382    
383            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
384            make tril(), triu(), band() work for "matrix" and all "dense*"
385    
386            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
387            * tests/simple.R: test the fix above
388    
389            * R/sparseMatrix.R ([): simplification: no coerce to <general>
390                    before we use as(., <Tsparse>)[...] anyway
391    
392            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
393    
394            * R/triangularMatrix.R (isTriangular): methods for all subclasses
395            instead of "triangularMatrix" -- just to disambiguate
396    
397    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
400            * tests/indexing.R: example that fails above
401    
402    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
405            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
406                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
407    
408            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
409            * src/Tsparse.h, init.c: ditto
410            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
411                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
412            * R/sparseMatrix.R (isTriangular): hence simplified
413    
414    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/Ops.R (.Arith.Csparse): new utility factored out of former
417              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
418    
419    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
422    
423            * inst/test-tools.R (isOrthogonal): new function; also file restructured
424    
425    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
428            coercion to "nMatrix" and "pMatrix"
429    
430            * R/AllClass.R: "Schur" class;  "number" class union
431            * man/number-class.Rd:
432            * man/Schur-class.Rd:
433    
434            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
435            (.simpleSchur): Schur() method for diagonal matrices
436            (.triSchur):    Schur() method for triangular matrices
437            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
438    
439    
440    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
443    
444    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
447                    in order to ensure 'system = *' is not lost;
448                    formals()$system instead of cut&paste.
449            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
450    
451    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * DESCRIPTION (Date): make ready for release --> 0.999375-4
454    
455            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
456    
457    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
460                    and hence does as.vector(.).
461            * man/pMatrix-class.Rd: docs
462            * R/sparseMatrix.R: fix for printing "integer sparse"
463    
464            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
465    
466            * R/Matrix.R and others: use "exact" function argument list for
467                    both "["   : (x, i,j, ..., drop)
468                    and  "[<-" : (x, i,j, ..., value)
469    
470            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
471            * R/Tsparse.R (replTmat):    ditto
472            * R/diagMatrix.R (replDiag): ditto
473            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
474            * tests/indexing.R: testing the above
475    
476    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/sparseMatrix.R (cov2cor): method for sparse matrices
479    
480            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
481    
482            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
483    
484            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
485    
486    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/Matrix.R: "generic" cov2cor() method
489    
490            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
491                    speed up Q %*% D %*% t(Q)
492            * tests/dpoMatrix.R: test nearPD()
493    
494    2007-12-05  Doug Bates and Martin Maechler
495    
496            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
497            stats::xtabs() allowing to create sparse matrices.
498    
499    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
502    
503    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
506    
507    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
508    
509            * R/LU.R: solve() method for "denseLU"
510    
511    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * DESCRIPTION (Version): 0.999375-3 preparing for release
514    
515            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
516    
517            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
518    
519    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
522              thanks to Kasper Kristensen.
523            * tests/matprod.R: regression test for that.
524    
525    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
526    
527            * [r4778] R/AllGeneric.R: Check R version before defining generics for
528              primitives
529    
530    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
531    
532            * R/denseMatrix.R (rcond): method
533            * R/sparseQR.R (rcond): method, use x or t(x)
534    
535    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
538            matrices.
539            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
540    
541            * man/rcond.Rd: mention the more general definition, and add
542            example for non-square matrices.
543    
544            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
545    
546    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
549    
550    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
551    
552            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
553            * tests/indexing.R: add new regression for the above cases.
554    
555    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
556    
557            * src/Mutils.h (__sun): clause for alloca.h on Solaris
558    
559    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * DESCRIPTION (Date, Version): 0.999375-2
562    
563    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * R/HBMM.R (readMM): make work for pattern matrices as well
566    
567    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
568    
569            * [r4730] src/Mutils.h: declare alloca
570            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
571              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
572              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
573              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
574              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
575              methods; switch writeMM to use CHOLMOD code; repair readMM
576    
577    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
580            Oehlschlaegel's ... result type still to be discussed!
581    
582    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * man/image-methods.Rd: new, combining all image() methods
585    
586    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
587    
588            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
589            to work via dgC...
590    
591            * R/Matrix.R (Matrix): special treatment for "table" (S3)
592    
593    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * R/dgTMatrix.R (image): change defaults to
596                    aspect = "iso", colorkey = FALSE
597    
598    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
601            must copy its *expanded* x slot before LAPACK call.
602    
603            * tests/matprod.R: test the last days' changes.
604    
605    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
606    
607            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
608              as well as in sources
609            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
610              Lapack call
611    
612    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
615                    ("Matrix", "matrix") which is needed in some cases.
616            Ditto for solve().
617    
618            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
619            infinite recursion in dispatch for some cases.
620    
621    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
622    
623            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
624              so pointers match
625    
626    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * DESCRIPTION (Date): set ready for release -- 0.999375-1
629    
630    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
631    
632            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
633              src/chm_common.c, src/chm_common.h: Change API for
634              numeric_as_chm_dense and N_AS_CHM_DN
635    
636    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
639            * tests/matprod.R: regr.test for it
640    
641    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
644            * tests/group-methods.R: and regression-test it
645    
646    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
647    
648            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
649              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
650              triplet_to_sparse, documentation, use typedefs
651    
652    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
653    
654            * man/dpoMatrix-class.Rd: added 'corMatrix' example
655    
656            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
657            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
658            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
659    
660            * R/lsparseMatrix.R: bug fix in "all" method
661            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
662    
663            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
664            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
665                    + matrix |-> nMatrix coercion
666            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
667            * man/pMatrix-class.Rd: ditto
668    
669            * R/Matrix.R (Summary): method for non-dMatrix
670    
671            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
672            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
673                    test all Summary methods.
674    
675    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
676    
677            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
678    
679    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
680    
681            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
682    
683            * R/pMatrix.R (t?crossprod): methods for pMatrix
684    
685    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
686    
687            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
688    
689    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
690    
691            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
692              trying to fix a subtle bug - which has been somewhere else.
693    
694    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
695    
696            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
697              solve the bug
698    
699    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
700    
701            * src/dgCMatrix.c (compressed_to_TMatrix):
702    
703    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * src/Csparse.c (Rsparse_validate): new, to have some validity
706            checking for RsparseMatrix
707            * src/dgCMatrix.c (xRMatrix_validate): ditto
708            * src/dtCMatrix.c (tRMatrix_validate): ditto
709    
710    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
711    
712            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
713              lgRMatrix
714            * [r4568] DESCRIPTION: Prepare for bug-fix release
715            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
716              for declaration of cholmod_symmetry
717    
718    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
721            release.
722    
723    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
724    
725            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
726              functions - no longer used
727            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
728              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
729              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
730              Alloca
731    
732    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
733    
734            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
735              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
736              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
737              src/t_gCMatrix_colSums.c: more R_CheckStack()s
738    
739    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
740    
741            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
742              the required amount of memory then call M_numeric_as_chm_dense.
743            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
744              (like Calloc but calling alloca)
745    
746    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
747    
748            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
749            and extended with more sophisticated 'col.names' option.
750            * NAMESPACE: export  printSparseMatrix()
751            * man/printSpMatrix.Rd: document, incl. examples
752    
753    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
754    
755            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
756              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
757              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
758    
759    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
760    
761            * DESCRIPTION (Version): 0.99875-4
762    
763            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
764            some dimnames perservation.
765    
766            * R/dsTMatrix.R (t-method): keep dimnames
767            * R/dtTMatrix.R:  ditto
768    
769            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
770            and ncol(.) < 10
771    
772            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
773            from Mutils.h
774    
775            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
776            e.g. in as(<ngCMatrix>, "matrix")
777    
778    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
779    
780            * [r4529] .: Create a branch for the API changes from the 0.99875
781              series to the 0.999375 series
782            * [r4530] DESCRIPTION, inst/include/Matrix.h,
783              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
784              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
785              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
786              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
787              as_cholmod_x functions
788    
789    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
790    
791            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
792              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
793              to Comparisons
794    
795    >>>>>>> .merge-right.r4561
796    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
797    
798            * DESCRIPTION (Version): 0.99875-3 ready to be released.
799    
800            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
801    
802            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
803            that should also work in a future version of R.
804    
805    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
806    
807            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
808    
809            * R/sparseVector.R: more *sparseVector coercions, notably for
810            non - double ones.
811    
812    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
813    
814            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
815              notably the new ones building on the new .Call(.)s:
816    
817            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
818            all 4 of [dlin]gCMatrix_colSums().
819    
820    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
821    
822            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
823            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
824              result
825    
826    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
827    
828            * R/kronecker.R: fix typo (could lead to inf.recursion)
829            * test/simple.R: testing that
830    
831            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
832            method as well (which can have arguments, show() can't).
833    
834    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
835    
836            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
837              added dgCMatrix_colSums for [col,row][Sums,Means]
838    
839    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
840    
841            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
842              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
843              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
844            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
845              class
846            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
847              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
848              row names to store the levels - duh!  Added an example.
849    
850    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
851    
852            * src/Csparse.c (Csparse_validate): check for *repeated* entries
853            thanks to example from Christian Buchta; with a test here:
854            * tests/simple.R:
855    
856    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
857    
858            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
859            of colSums(*, sparseResult = TRUE)
860    
861    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
862    
863            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
864            'na.rm = FALSE' as "everywhere" else in R.
865    
866    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
867    
868            * [r4421] src/CSparse_install.sh: Modify for new organization of
869              CSparse package
870            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
871              SuiteSparse
872            * [r4426] src/Makefile: add ./UFconfig to the include path for
873              compilation
874            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
875            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
876              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
877    
878    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
881            * R/sparseMatrix.R (prSpMatrix): now gives a message about
882            suppressed column names.
883    
884    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
885    
886            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
887              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
888              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
889              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
890              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
891              Remove warnings after change to const char* CHAR
892    
893    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
894    
895            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
896              type of M_cholmod_ssmult
897    
898    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
899    
900            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
901              src/init.c: Yet another cholmod export - cholmod_ssmult
902    
903    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
904    
905            * NAMESPACE: exported drop0(), since
906            * man/drop0.Rd: I have seen several cases, I really wanted to use
907            it, so our users may want too.
908    
909    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
910    
911            * man/colSums.Rd: separately document colSums() etc, since these
912            have the extra argument 'sparseResult'.
913    
914    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
915    
916            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
917            * man/spMatrix.Rd: docu., including examples
918    
919            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
920            in order to make colMeans() etc fast *and* correct.
921            * R/sparseVector.R (replSPvec): "[<-" functionality for
922            sparseVectors; tested in
923            * tests/simple.R:
924    
925    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
926    
927            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
928            (very) sparse Matrices; output similar to Matlab's print().
929    
930    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
931    
932            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
933            0-based, indices (Jose Quesada <quesada@gmail.com>).
934    
935    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
936    
937            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
938    
939    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
940    
941            * R/Auxiliaries.R (sparsapply): new utility, much faster than
942            tapply1() for large sparse matrices.
943    
944    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
945    
946            * R/Matrix.R (dim<-): reshape now via sparseVector.
947    
948            * R/sparseVector.R: methods and function for
949            * R/AllClass.R: new "sparseVector" class and daughters.
950            * NAMESPACE: export new classes
951    
952    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
953    
954            * DESCRIPTION (Version): 0.99875-1
955            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
956    
957    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
958    
959            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
960            indexing
961            * tests/indexing.R: test set for that.
962    
963    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
964    
965            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
966            entries.
967            * tests/indexing.R(out): add regression test for it
968    
969    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
970    
971            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
972            name for "!" method definitions.
973    
974    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
975    
976            * R/Tsparse.R (intI): new utility, used for "[" :
977                    Cleanup up there, and fixes for duplicated indices - more TODO!
978    
979            * tests/indexing.R(out): more tests
980    
981    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
982    
983            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
984            code that is now part of the R Lapack library.
985    
986            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
987            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
988    
989    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
990    
991            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
992    
993    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
994    
995            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
996            up with extraneous names '0'...'<n-1>'
997    
998    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
999    
1000            * R/dgTMatrix.R (mat2dgT): care about NAs
1001    
1002    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1003    
1004            * R/kronecker.R: triangularity preserving methods
1005    
1006    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1007    
1008            * R/kronecker.R: new file collecting kronecker() methods in one
1009                    place.  Goal: become much faster!
1010    
1011    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1012    
1013            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1014            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1015            can be much faster.
1016    
1017            * tests/matprod.R: add regression tests for these (upper & lower).
1018    
1019    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
1021            * R/Matrix.R (diff): method for our Matrices.
1022    
1023            * R/sparseMatrix.R (isDiagonal): check dim()!
1024    
1025    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1026    
1027            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1028            proposal from Tamas Papp.
1029    
1030    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1031    
1032            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1033    
1034            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1035            rather define and export  cBind() and rBind() only.
1036            --> useRs *must* change code that used to have cbind()/rbind() !!
1037    
1038            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1039            * R/bind.Rout.save: ditto
1040    
1041    2007-02-16  Douglas Bates  <bates@r-project.org>
1042    
1043            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1044            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1045            const modifier on declaration of the array 'valid'
1046    
1047    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1048    
1049            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1050    
1051    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1052    
1053            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1054    
1055            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1056            * tests/simple.R: test the above and some of these coercions:
1057    
1058            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1059                    be careful to avoid infinite recursion, using new coercions in
1060            * R/ngCMatrix.R and nsC... and ntC...
1061            * R/lsparseMatrix.R: ditto
1062    
1063            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1064    
1065            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1066            * R/Rsparse.R: reactivate .Call()s
1067    
1068            * tests/Class+Meth.R: a bit more on actual classes
1069    
1070    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1071    
1072            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1073    
1074    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1075    
1076            * DESCRIPTION (Version): 0.9975-10 to upload
1077    
1078            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1079            specific classes less unconditionally.
1080    
1081            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1082    
1083            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1084    
1085            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1086            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1087            R_to_CMatrix segfaults on one platform.
1088            Eliminate most coercion method to *specific* classes, and replace
1089            with virtual classes coercions.
1090    
1091    
1092    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1093    
1094            * src/init.c: export the CHM...._validate() placeholders, since
1095            they *are* called.
1096    
1097            * tests/Class+Meth.R (classCanCoerce): and starting to test
1098            all as(<from>, <to>)
1099    
1100    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1101    
1102            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1103            * tests/indexing.R: tested now
1104            * tests/indexing.Rout.save: updated
1105    
1106            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1107            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1108            appropriate.
1109    
1110            * NAMESPACE: export a trivial
1111            * R/Matrix.R: drop() Matrix-method
1112    
1113            * R/AllClass.R: moved all prototypes to virtual super classes.
1114    
1115            * R/Rsparse.R: many more coercions to have less exceptions in
1116            * tests/Class+Meth.R:
1117    
1118            * R/Ops.R (Compare): tweak for case with NA
1119            * tests/simpl.R: hence another 'FIXME' eliminated
1120    
1121    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1122    
1123            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1124            objects.
1125    
1126            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1127              and more of "!", "&", "|", all, any; coercions
1128    
1129            * R/Rsparse.R: many coercions (which enable quite a few other
1130            methods), thanks to enhancements in
1131            * src/dgCMatrix.c (R_to_CMatrix): new, and
1132            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1133            symmetric & triangular and ..RMatrix objects.
1134    
1135            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1136            renamed file from src/dsTMatrix.c;
1137            now dealing with symmetric and triangular Tsparse coercions, both
1138            to dense and general.
1139    
1140    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1141    
1142            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1143    
1144            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1145            where sensible when the <numeric> is of length > 1.
1146    
1147    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1148    
1149            * R/Matrix.R ([<-): for M[] <- value: fix length
1150    
1151    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1152    
1153            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1154            * R/ndenseMatrix.R: new coercions n* -> l*
1155    
1156    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1157    
1158            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1159    
1160            * R/Ops.R ("Logic"): and other "Ops", many updates
1161    
1162    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1163    
1164            * src/Mutils.h (SET_DimNames): new utility
1165    
1166            * R/Auxiliaries.R (nnzero): improved and now exported via
1167    
1168            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1169    
1170    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1171    
1172            * R/diagMatrix.R (!): fix typo.
1173    
1174    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1175    
1176            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1177                    allow to pass class definition --> speedup
1178            * R/sparseMatrix.R: apply the above
1179    
1180            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1181    
1182            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1183            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1184            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1185    
1186            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1187    
1188            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1189            and use it for "sparse*" as well, since it's faster than the
1190            as_Csparse(.) way.
1191    
1192    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1193    
1194            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1195    
1196    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1197    
1198            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1199            as method for   M[ ij ] <- v
1200            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1201    
1202            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1203            FALSE answer
1204    
1205            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1206            * tests/indexing.R: test it, and some of the above
1207    
1208    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1209    
1210            * R/Auxiliaries.R (is_duplicatedT): new utility
1211    
1212    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1213    
1214            * src/init.c (R_init_Matrix): export cholmod_scale
1215    
1216    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1217    
1218            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1219            base::as.matrix to (x, ...)
1220    
1221    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1222    
1223            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1224            file; start using "Logic", hence
1225    
1226            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1227            * NAMESPACE: import and export "Logic"
1228    
1229    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1230    
1231            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1232            only needed previously to R version 2.5.0.
1233    
1234    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1235    
1236            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1237    
1238            * R/Tsparse.R (replTmat): fix subassignment of triangular
1239            * R/Csparse.R (replCmat): ditto
1240            * tests/indexing.R: more tests, incl the above fix
1241    
1242    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1243    
1244            * R/Auxiliaries.R (drop0): extend for non CSparse
1245            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1246    
1247            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1248                    use uplo correctly (!); other places: use uplo_P() macro
1249    
1250            * R/Csparse.R (replCmat): call diagU2N() when needed
1251            * R/Tsparse.R (replTmat): ditto
1252    
1253            * src/dtCMatrix.c (tCMatrix_validate): new
1254            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1255            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1256    
1257            * R/diagMatrix.R (replDiag): to use in [<-
1258    
1259    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1260    
1261            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1262                    also more general diagU2N().
1263    
1264    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1265    
1266            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1267            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1268    
1269    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1270    
1271            * tests/bind.R: a few more cases
1272            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1273    
1274            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1275            * R/ddenseMatrix.R (cbind2/rbind2)
1276            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1277            * tests/indexing.R
1278            * tests/indexing.Rout.save: updated
1279    
1280    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1281    
1282            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1283            * tests/indexing.R
1284    
1285    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1286    
1287            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1288            align with proper position of "0", i.e., right for integers.
1289            argument 'align' by default is "fancy".
1290    
1291    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1292    
1293            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1294            * R/Csparse.R: and fix "Compare" for more cases.
1295            * tests/Class+Meth.R: test some of these (m == m, m != m)
1296    
1297    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1298    
1299            * R/lsparseMatrix.R: all() and any() methods
1300            * R/ldenseMatrix.R:      ditto
1301            * NAMESPACE, R/Matrix.R: ditto
1302    
1303            * man/all-methods.Rd: document them minimally
1304    
1305            * tests/simple.R: add a few examples for these
1306    
1307    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1308    
1309            * R/Tsparse.R ([): fix long standing typo in symmetric case
1310            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1311    
1312    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1313    
1314            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1315            to LL before converting to a sparse matrix. (The LDL form can be
1316            converted to a sparse matrix but it is implicitly a unit
1317            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1318    
1319    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1320    
1321            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1322    
1323    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1324    
1325            * DESCRIPTION (Version): updated -> release 0.9975-7
1326            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1327    
1328  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1329    
1330          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method

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