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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 2188, Mon Apr 28 13:42:12 2008 UTC
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1    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
4            for R < 2.7.0.
5    
6            * R/Tsparse.R ([): for triangularMatrix, check if result may be
7            triangular.
8            * tests/indexing.R: regression test
9    
10    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
13            * R/Ops.R: more methods, for lMatrix/nMatrix
14    
15    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/expm.R: new file for all expm() methods; notably new ones for
18            diagonal*, triangular*, symmetric* and also simple "matrix".
19    
20    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
23    
24            * inst/test-tools.R (assert.EQ.mat): better message when not equal
25    
26            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
27    
28            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
29            [dl]denseMatrix {identical slots; but more logical method dispatch}
30    
31    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
34    
35            * R/diagMatrix.R (determinant): method
36    
37    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
40    
41            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
42    
43            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
44            its diagonal
45    
46    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
49    
50            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
51    
52            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
53    
54            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
55    
56    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
59    
60            * R/Ops.R (.do.Logic.lsparse): fix NA case
61    
62            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
63    
64            * R/Auxiliaries.R (nnzero): fix special cases, using
65            * R/Auxiliaries.R (indDiag): new utility
66            * R/Auxiliaries.R (indTri): new argument 'diag'
67    
68            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
69    
70    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
73    
74            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
75            ".tCMatrix" triangular matrix.
76    
77            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
78            'clx' can be class *or* class representation.
79            (nnzSparse): new.
80            (non0ind): new 'xtendSymm' argument; used in
81            * R/Ops.R:
82    
83            * R/pMatrix.R: more efficient determinant() method
84    
85    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
88            * [disactivated] NAMESPACE: export(det)
89    
90            * R/diagMatrix.R (mkDiag): new substitute for diag()
91    
92            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
93            (as0, as1): new utility.
94    
95            * R/Csparse.R (diag, band): need diagU2N()
96    
97            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
98    
99            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
100    
101            * R/Ops.R (Compare): fix <nsp> o <nsp> case
102    
103            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
104    
105    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/Auxiliaries.R (signPerm): new utility for
108            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
109    
110            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
111            since we have our own error handler (and can use tryCatch() from R).
112    
113    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
116    
117            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
118            when not positive definite.
119    
120            * R/Auxiliaries.R (asTri): new auxiliary
121            (non0.i): make *much* faster for Tsparse with many non-zero
122            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
123    
124            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
125            test-tools.R , see below
126    
127            * R/dMatrix.R: fix "Summary" method: + diagU2N()
128    
129            * NAMESPACE, R/Matrix.R: add mean() method
130    
131    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
134            cold-hot colors; try *changed* default useAbs = FALSE
135            * man/image-methods.Rd:  nice examples
136    
137    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * inst/test-tools.R (checkMatrix): new function for modularizing part
140            of tstMatrixClass() in tests/Class+Meth.R
141    
142            * R/dsCMatrix.R: coercion from "matrix"
143            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
144    
145            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
146            add test for as(matrix(,0,0), <class>)
147    
148    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
151            work as determinant(matrix(,0,0)).
152    
153            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
154            * man/sparseLU-class.Rd: ditto
155    
156            * R/dgCMatrix.R (determinant): method building on lu()
157            * R/sparseMatrix.R, Matrix.R, ...: ditto
158    
159            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
160    
161    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
164            pattern matrices.
165    
166    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * src/dense.c (dense_to_Csparse): all declarations *before*
169            R_CheckStack(); needed e.g. for ancient gcc 2.96.
170    
171    
172    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * DESCRIPTION (Version): 0.999375-9 --- need to release
175            for R-devel (and R 2.7.0 alpha soon).
176    
177            * R/AllClass.R: drop "double" from "atomicVector" class union
178    
179            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
180            * R/dgeMatrix.R: ditto
181    
182            * R/sparseMatrix.R (summary): count NAs
183    
184            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
185    
186    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
189            order to become compatible to new R 2.7.0 base::rcond().
190    
191    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
194    
195            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
196    
197            * inst/test-tools.R (isValid): new utility, used much in
198            * tests/simple.R:
199    
200            * man/BunchKaufman-methods.Rd: added too
201    
202    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/dsyMatrix.R: add BunchKaufman() methods.
205            * R/dspMatrix.R:
206    
207            * src/init.c: add dsyMatrix_trf
208    
209    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
210    
211            * DESCRIPTION (Version): release 0.999375-7
212            * src/CHMfactor.c (CHMfactor_update): fix
213    
214    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
217            internal_chm_factor().
218    
219            * R/AllGeneric.R: do *not* define a "chol" generic
220                    (but rather use the implicit one *without* making pivot
221                    part of the signature)
222            * R/*.R: drop the 'pivot' from chol's signature and make
223                    'pivot=FALSE' a default argument of method definitions.
224    
225            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
226            version of Matrix
227    
228    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
231    
232            * R/sparseMatrix.R (is.na): new simple method
233            * R/denseMatrix.R (is.na): ditto.
234    
235            * R/diagMatrix.R (.symDiagonal): newly exported utility.
236    
237            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
238    
239            * src/UFsparse_download.sh: -->
240            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
241    
242    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
245            functionality; barely tested in
246            * tests/factorizing.R
247    
248            * src/Csparse.c (diag_tC): new functionality to enable faster
249            determinant(<dsCMatrix>, .) in
250            * R/dsCMatrix.R
251    
252    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
253    
254            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
255              src/CHMfactor.c, src/CHMfactor.h,
256              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
257              Log-determinant of the parent matrix from a CHMfactor object as
258              chm_factor_ldetL2; documentation and support
259    
260    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
263    
264    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
267            warning.
268    
269    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
272    
273            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
274              <diagonal> o <sparse_triangular>
275              setAs(., "nMatrix") added.
276    
277            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
278    
279            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
280                    new argument 'checkDense = FALSE'.
281    
282    
283    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
286            back-permutation of the matrix exponential.
287    
288            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
289    
290            * DESCRIPTION (Date,Version): ready to release 0.999375-5
291    
292            * tests/simple.R: testing diagN2U
293    
294    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/Auxiliaries.R (diagN2U): interface to
297    
298            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
299    
300            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
301    
302    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * src/chm_common.c (chm_diagN2U): new utility.
305    
306            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
307            make use of chm_diagN2U() and hence now preserve triangularity and
308            unit-triangularity.
309    
310            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
311    
312    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
315    
316            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
317            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
318    
319            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
320    
321            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
322    
323            * src/chm_common.c (AS_CHM_FINISH): add note about problem
324            for triangular (diag = "U").
325    
326    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
329            * R/bind.R:  .Call(dense_to_Csparse, *)
330    
331    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * R/Matrix.R (Matrix): no longer use coercions to specific classes
334                    (since we are discouraging them in user code).
335    
336            * tests/*.R: also replaces coercions to specific classes by
337            coercions to super classes.
338    
339            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
340    
341    
342    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
345    
346            * src/dense.c (dense_band): generalized from ddense_band
347    
348            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
349              now for "denseMatrix" (instead of just "ddense*"); much
350              simplified setMethod()s for these.
351    
352            * src/dense.c (dense_to_symmetric): generalized from ddense_*
353    
354    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
357            version of as(*, "symmetricMatric").
358    
359            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
360            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
361    
362    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * R/Matrix.R (subset.ij): utility, as first step to faster
365               M [ <ij-matrix> ] indexing.
366    
367            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
368    
369            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
370            for more efficient symmpart() and skewpart() methods.
371    
372            * src/Mutils.c (equal_string_vectors): utility
373    
374            * src/dense.c (ddense_to_symmetric): new function used in
375    
376            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
377    
378            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
379            order to match the generic (and evade .local(..)).
380    
381            * R/dsCMatrix.R: dgC -> dsC: use C code!
382    
383            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
384            as per TODO
385    
386            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
387    
388            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
389    
390    
391    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
394    
395            * R/Auxiliaries.R (non0.i): take out of non0ind
396    
397            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
398            make tril(), triu(), band() work for "matrix" and all "dense*"
399    
400            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
401            * tests/simple.R: test the fix above
402    
403            * R/sparseMatrix.R ([): simplification: no coerce to <general>
404                    before we use as(., <Tsparse>)[...] anyway
405    
406            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
407    
408            * R/triangularMatrix.R (isTriangular): methods for all subclasses
409            instead of "triangularMatrix" -- just to disambiguate
410    
411    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
414            * tests/indexing.R: example that fails above
415    
416    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
419            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
420                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
421    
422            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
423            * src/Tsparse.h, init.c: ditto
424            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
425                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
426            * R/sparseMatrix.R (isTriangular): hence simplified
427    
428    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430            * R/Ops.R (.Arith.Csparse): new utility factored out of former
431              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
432    
433    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
436    
437            * inst/test-tools.R (isOrthogonal): new function; also file restructured
438    
439    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
442            coercion to "nMatrix" and "pMatrix"
443    
444            * R/AllClass.R: "Schur" class;  "number" class union
445            * man/number-class.Rd:
446            * man/Schur-class.Rd:
447    
448            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
449            (.simpleSchur): Schur() method for diagonal matrices
450            (.triSchur):    Schur() method for triangular matrices
451            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
452    
453    
454    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
455    
456            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
457    
458    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
461                    in order to ensure 'system = *' is not lost;
462                    formals()$system instead of cut&paste.
463            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
464    
465    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * DESCRIPTION (Date): make ready for release --> 0.999375-4
468    
469            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
470    
471    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
472    
473            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
474                    and hence does as.vector(.).
475            * man/pMatrix-class.Rd: docs
476            * R/sparseMatrix.R: fix for printing "integer sparse"
477    
478            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
479    
480            * R/Matrix.R and others: use "exact" function argument list for
481                    both "["   : (x, i,j, ..., drop)
482                    and  "[<-" : (x, i,j, ..., value)
483    
484            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
485            * R/Tsparse.R (replTmat):    ditto
486            * R/diagMatrix.R (replDiag): ditto
487            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
488            * tests/indexing.R: testing the above
489    
490    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/sparseMatrix.R (cov2cor): method for sparse matrices
493    
494            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
495    
496            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
497    
498            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
499    
500    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * R/Matrix.R: "generic" cov2cor() method
503    
504            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
505                    speed up Q %*% D %*% t(Q)
506            * tests/dpoMatrix.R: test nearPD()
507    
508    2007-12-05  Doug Bates and Martin Maechler
509    
510            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
511            stats::xtabs() allowing to create sparse matrices.
512    
513    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
516    
517    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
520    
521    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
522    
523            * R/LU.R: solve() method for "denseLU"
524    
525    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * DESCRIPTION (Version): 0.999375-3 preparing for release
528    
529            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
530    
531            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
532    
533    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
536              thanks to Kasper Kristensen.
537            * tests/matprod.R: regression test for that.
538    
539    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
540    
541            * [r4778] R/AllGeneric.R: Check R version before defining generics for
542              primitives
543    
544    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
545    
546            * R/denseMatrix.R (rcond): method
547            * R/sparseQR.R (rcond): method, use x or t(x)
548    
549    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
552            matrices.
553            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
554    
555            * man/rcond.Rd: mention the more general definition, and add
556            example for non-square matrices.
557    
558            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
559    
560    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
563    
564    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
565    
566            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
567            * tests/indexing.R: add new regression for the above cases.
568    
569    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * src/Mutils.h (__sun): clause for alloca.h on Solaris
572    
573    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
574    
575            * DESCRIPTION (Date, Version): 0.999375-2
576    
577    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * R/HBMM.R (readMM): make work for pattern matrices as well
580    
581    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
582    
583            * [r4730] src/Mutils.h: declare alloca
584            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
585              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
586              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
587              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
588              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
589              methods; switch writeMM to use CHOLMOD code; repair readMM
590    
591    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
594            Oehlschlaegel's ... result type still to be discussed!
595    
596    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * man/image-methods.Rd: new, combining all image() methods
599    
600    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
601    
602            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
603            to work via dgC...
604    
605            * R/Matrix.R (Matrix): special treatment for "table" (S3)
606    
607    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * R/dgTMatrix.R (image): change defaults to
610                    aspect = "iso", colorkey = FALSE
611    
612    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
615            must copy its *expanded* x slot before LAPACK call.
616    
617            * tests/matprod.R: test the last days' changes.
618    
619    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
620    
621            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
622              as well as in sources
623            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
624              Lapack call
625    
626    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
629                    ("Matrix", "matrix") which is needed in some cases.
630            Ditto for solve().
631    
632            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
633            infinite recursion in dispatch for some cases.
634    
635    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
636    
637            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
638              so pointers match
639    
640    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * DESCRIPTION (Date): set ready for release -- 0.999375-1
643    
644    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
645    
646            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
647              src/chm_common.c, src/chm_common.h: Change API for
648              numeric_as_chm_dense and N_AS_CHM_DN
649    
650    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
653            * tests/matprod.R: regr.test for it
654    
655    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
658            * tests/group-methods.R: and regression-test it
659    
660    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
661    
662            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
663              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
664              triplet_to_sparse, documentation, use typedefs
665    
666    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * man/dpoMatrix-class.Rd: added 'corMatrix' example
669    
670            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
671            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
672            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
673    
674            * R/lsparseMatrix.R: bug fix in "all" method
675            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
676    
677            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
678            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
679                    + matrix |-> nMatrix coercion
680            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
681            * man/pMatrix-class.Rd: ditto
682    
683            * R/Matrix.R (Summary): method for non-dMatrix
684    
685            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
686            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
687                    test all Summary methods.
688    
689    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
690    
691            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
692    
693    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
696    
697            * R/pMatrix.R (t?crossprod): methods for pMatrix
698    
699    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
700    
701            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
702    
703    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
704    
705            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
706              trying to fix a subtle bug - which has been somewhere else.
707    
708    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
709    
710            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
711              solve the bug
712    
713    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * src/dgCMatrix.c (compressed_to_TMatrix):
716    
717    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
718    
719            * src/Csparse.c (Rsparse_validate): new, to have some validity
720            checking for RsparseMatrix
721            * src/dgCMatrix.c (xRMatrix_validate): ditto
722            * src/dtCMatrix.c (tRMatrix_validate): ditto
723    
724    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
725    
726            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
727              lgRMatrix
728            * [r4568] DESCRIPTION: Prepare for bug-fix release
729            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
730              for declaration of cholmod_symmetry
731    
732    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
735            release.
736    
737    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
738    
739            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
740              functions - no longer used
741            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
742              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
743              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
744              Alloca
745    
746    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
747    
748            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
749              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
750              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
751              src/t_gCMatrix_colSums.c: more R_CheckStack()s
752    
753    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
754    
755            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
756              the required amount of memory then call M_numeric_as_chm_dense.
757            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
758              (like Calloc but calling alloca)
759    
760    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
761    
762            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
763            and extended with more sophisticated 'col.names' option.
764            * NAMESPACE: export  printSparseMatrix()
765            * man/printSpMatrix.Rd: document, incl. examples
766    
767    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
768    
769            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
770              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
771              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
772    
773    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * DESCRIPTION (Version): 0.99875-4
776    
777            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
778            some dimnames perservation.
779    
780            * R/dsTMatrix.R (t-method): keep dimnames
781            * R/dtTMatrix.R:  ditto
782    
783            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
784            and ncol(.) < 10
785    
786            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
787            from Mutils.h
788    
789            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
790            e.g. in as(<ngCMatrix>, "matrix")
791    
792    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
793    
794            * [r4529] .: Create a branch for the API changes from the 0.99875
795              series to the 0.999375 series
796            * [r4530] DESCRIPTION, inst/include/Matrix.h,
797              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
798              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
799              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
800              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
801              as_cholmod_x functions
802    
803    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
804    
805            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
806              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
807              to Comparisons
808    
809    >>>>>>> .merge-right.r4561
810    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
811    
812            * DESCRIPTION (Version): 0.99875-3 ready to be released.
813    
814            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
815    
816            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
817            that should also work in a future version of R.
818    
819    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
820    
821            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
822    
823            * R/sparseVector.R: more *sparseVector coercions, notably for
824            non - double ones.
825    
826    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
827    
828            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
829              notably the new ones building on the new .Call(.)s:
830    
831            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
832            all 4 of [dlin]gCMatrix_colSums().
833    
834    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
835    
836            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
837            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
838              result
839    
840    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
841    
842            * R/kronecker.R: fix typo (could lead to inf.recursion)
843            * test/simple.R: testing that
844    
845            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
846            method as well (which can have arguments, show() can't).
847    
848    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
849    
850            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
851              added dgCMatrix_colSums for [col,row][Sums,Means]
852    
853    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
854    
855            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
856              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
857              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
858            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
859              class
860            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
861              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
862              row names to store the levels - duh!  Added an example.
863    
864    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
865    
866            * src/Csparse.c (Csparse_validate): check for *repeated* entries
867            thanks to example from Christian Buchta; with a test here:
868            * tests/simple.R:
869    
870    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
871    
872            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
873            of colSums(*, sparseResult = TRUE)
874    
875    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
876    
877            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
878            'na.rm = FALSE' as "everywhere" else in R.
879    
880    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
881    
882            * [r4421] src/CSparse_install.sh: Modify for new organization of
883              CSparse package
884            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
885              SuiteSparse
886            * [r4426] src/Makefile: add ./UFconfig to the include path for
887              compilation
888            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
889            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
890              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
891    
892    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
893    
894            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
895            * R/sparseMatrix.R (prSpMatrix): now gives a message about
896            suppressed column names.
897    
898    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
899    
900            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
901              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
902              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
903              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
904              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
905              Remove warnings after change to const char* CHAR
906    
907    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
908    
909            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
910              type of M_cholmod_ssmult
911    
912    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
913    
914            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
915              src/init.c: Yet another cholmod export - cholmod_ssmult
916    
917    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
918    
919            * NAMESPACE: exported drop0(), since
920            * man/drop0.Rd: I have seen several cases, I really wanted to use
921            it, so our users may want too.
922    
923    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
924    
925            * man/colSums.Rd: separately document colSums() etc, since these
926            have the extra argument 'sparseResult'.
927    
928    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
929    
930            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
931            * man/spMatrix.Rd: docu., including examples
932    
933            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
934            in order to make colMeans() etc fast *and* correct.
935            * R/sparseVector.R (replSPvec): "[<-" functionality for
936            sparseVectors; tested in
937            * tests/simple.R:
938    
939    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
940    
941            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
942            (very) sparse Matrices; output similar to Matlab's print().
943    
944    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
945    
946            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
947            0-based, indices (Jose Quesada <quesada@gmail.com>).
948    
949    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
950    
951            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
952    
953    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
954    
955            * R/Auxiliaries.R (sparsapply): new utility, much faster than
956            tapply1() for large sparse matrices.
957    
958    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
959    
960            * R/Matrix.R (dim<-): reshape now via sparseVector.
961    
962            * R/sparseVector.R: methods and function for
963            * R/AllClass.R: new "sparseVector" class and daughters.
964            * NAMESPACE: export new classes
965    
966    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
967    
968            * DESCRIPTION (Version): 0.99875-1
969            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
970    
971    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
972    
973            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
974            indexing
975            * tests/indexing.R: test set for that.
976    
977    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
978    
979            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
980            entries.
981            * tests/indexing.R(out): add regression test for it
982    
983    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
984    
985            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
986            name for "!" method definitions.
987    
988    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
989    
990            * R/Tsparse.R (intI): new utility, used for "[" :
991                    Cleanup up there, and fixes for duplicated indices - more TODO!
992    
993            * tests/indexing.R(out): more tests
994    
995    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
996    
997            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
998            code that is now part of the R Lapack library.
999    
1000            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1001            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1002    
1003    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1004    
1005            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1006    
1007    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1008    
1009            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1010            up with extraneous names '0'...'<n-1>'
1011    
1012    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1013    
1014            * R/dgTMatrix.R (mat2dgT): care about NAs
1015    
1016    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1017    
1018            * R/kronecker.R: triangularity preserving methods
1019    
1020    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1021    
1022            * R/kronecker.R: new file collecting kronecker() methods in one
1023                    place.  Goal: become much faster!
1024    
1025    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1026    
1027            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1028            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1029            can be much faster.
1030    
1031            * tests/matprod.R: add regression tests for these (upper & lower).
1032    
1033    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1034    
1035            * R/Matrix.R (diff): method for our Matrices.
1036    
1037            * R/sparseMatrix.R (isDiagonal): check dim()!
1038    
1039    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1040    
1041            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1042            proposal from Tamas Papp.
1043    
1044    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1045    
1046            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1047    
1048            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1049            rather define and export  cBind() and rBind() only.
1050            --> useRs *must* change code that used to have cbind()/rbind() !!
1051    
1052            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1053            * R/bind.Rout.save: ditto
1054    
1055    2007-02-16  Douglas Bates  <bates@r-project.org>
1056    
1057            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1058            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1059            const modifier on declaration of the array 'valid'
1060    
1061    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1062    
1063            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1064    
1065    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1066    
1067            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1068    
1069            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1070            * tests/simple.R: test the above and some of these coercions:
1071    
1072            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1073                    be careful to avoid infinite recursion, using new coercions in
1074            * R/ngCMatrix.R and nsC... and ntC...
1075            * R/lsparseMatrix.R: ditto
1076    
1077            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1078    
1079            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1080            * R/Rsparse.R: reactivate .Call()s
1081    
1082            * tests/Class+Meth.R: a bit more on actual classes
1083    
1084    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1085    
1086            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1087    
1088    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1089    
1090            * DESCRIPTION (Version): 0.9975-10 to upload
1091    
1092            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1093            specific classes less unconditionally.
1094    
1095            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1096    
1097            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1098    
1099            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1100            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1101            R_to_CMatrix segfaults on one platform.
1102            Eliminate most coercion method to *specific* classes, and replace
1103            with virtual classes coercions.
1104    
1105    
1106    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1107    
1108            * src/init.c: export the CHM...._validate() placeholders, since
1109            they *are* called.
1110    
1111            * tests/Class+Meth.R (classCanCoerce): and starting to test
1112            all as(<from>, <to>)
1113    
1114    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1115    
1116            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1117            * tests/indexing.R: tested now
1118            * tests/indexing.Rout.save: updated
1119    
1120            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1121            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1122            appropriate.
1123    
1124            * NAMESPACE: export a trivial
1125            * R/Matrix.R: drop() Matrix-method
1126    
1127            * R/AllClass.R: moved all prototypes to virtual super classes.
1128    
1129            * R/Rsparse.R: many more coercions to have less exceptions in
1130            * tests/Class+Meth.R:
1131    
1132            * R/Ops.R (Compare): tweak for case with NA
1133            * tests/simpl.R: hence another 'FIXME' eliminated
1134    
1135    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1136    
1137            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1138            objects.
1139    
1140            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1141              and more of "!", "&", "|", all, any; coercions
1142    
1143            * R/Rsparse.R: many coercions (which enable quite a few other
1144            methods), thanks to enhancements in
1145            * src/dgCMatrix.c (R_to_CMatrix): new, and
1146            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1147            symmetric & triangular and ..RMatrix objects.
1148    
1149            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1150            renamed file from src/dsTMatrix.c;
1151            now dealing with symmetric and triangular Tsparse coercions, both
1152            to dense and general.
1153    
1154    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1155    
1156            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1157    
1158            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1159            where sensible when the <numeric> is of length > 1.
1160    
1161    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1162    
1163            * R/Matrix.R ([<-): for M[] <- value: fix length
1164    
1165    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1166    
1167            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1168            * R/ndenseMatrix.R: new coercions n* -> l*
1169    
1170    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1171    
1172            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1173    
1174            * R/Ops.R ("Logic"): and other "Ops", many updates
1175    
1176    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1177    
1178            * src/Mutils.h (SET_DimNames): new utility
1179    
1180            * R/Auxiliaries.R (nnzero): improved and now exported via
1181    
1182            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1183    
1184    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1185    
1186            * R/diagMatrix.R (!): fix typo.
1187    
1188    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1189    
1190            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1191                    allow to pass class definition --> speedup
1192            * R/sparseMatrix.R: apply the above
1193    
1194            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1195    
1196            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1197            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1198            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1199    
1200            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1201    
1202            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1203            and use it for "sparse*" as well, since it's faster than the
1204            as_Csparse(.) way.
1205    
1206    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1207    
1208            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1209    
1210    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1211    
1212            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1213            as method for   M[ ij ] <- v
1214            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1215    
1216            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1217            FALSE answer
1218    
1219            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1220            * tests/indexing.R: test it, and some of the above
1221    
1222    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1223    
1224            * R/Auxiliaries.R (is_duplicatedT): new utility
1225    
1226    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1227    
1228            * src/init.c (R_init_Matrix): export cholmod_scale
1229    
1230    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1231    
1232            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1233            base::as.matrix to (x, ...)
1234    
1235    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1236    
1237            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1238            file; start using "Logic", hence
1239    
1240            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1241            * NAMESPACE: import and export "Logic"
1242    
1243    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1244    
1245            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1246            only needed previously to R version 2.5.0.
1247    
1248    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1249    
1250            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1251    
1252            * R/Tsparse.R (replTmat): fix subassignment of triangular
1253            * R/Csparse.R (replCmat): ditto
1254            * tests/indexing.R: more tests, incl the above fix
1255    
1256    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1257    
1258            * R/Auxiliaries.R (drop0): extend for non CSparse
1259            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1260    
1261            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1262                    use uplo correctly (!); other places: use uplo_P() macro
1263    
1264            * R/Csparse.R (replCmat): call diagU2N() when needed
1265            * R/Tsparse.R (replTmat): ditto
1266    
1267            * src/dtCMatrix.c (tCMatrix_validate): new
1268            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1269            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1270    
1271            * R/diagMatrix.R (replDiag): to use in [<-
1272    
1273    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1274    
1275            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1276                    also more general diagU2N().
1277    
1278    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1279    
1280            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1281            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1282    
1283    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1284    
1285            * tests/bind.R: a few more cases
1286            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1287    
1288            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1289            * R/ddenseMatrix.R (cbind2/rbind2)
1290            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1291            * tests/indexing.R
1292            * tests/indexing.Rout.save: updated
1293    
1294    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1295    
1296            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1297            * tests/indexing.R
1298    
1299    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1300    
1301            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1302            align with proper position of "0", i.e., right for integers.
1303            argument 'align' by default is "fancy".
1304    
1305    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1306    
1307            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1308            * R/Csparse.R: and fix "Compare" for more cases.
1309            * tests/Class+Meth.R: test some of these (m == m, m != m)
1310    
1311    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1312    
1313            * R/lsparseMatrix.R: all() and any() methods
1314            * R/ldenseMatrix.R:      ditto
1315            * NAMESPACE, R/Matrix.R: ditto
1316    
1317            * man/all-methods.Rd: document them minimally
1318    
1319            * tests/simple.R: add a few examples for these
1320    
1321    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1322    
1323            * R/Tsparse.R ([): fix long standing typo in symmetric case
1324            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1325    
1326    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1327    
1328            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1329            to LL before converting to a sparse matrix. (The LDL form can be
1330            converted to a sparse matrix but it is implicitly a unit
1331            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1332    
1333    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1334    
1335            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1336    
1337    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1338    
1339            * DESCRIPTION (Version): updated -> release 0.9975-7
1340            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1341    
1342    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1343    
1344            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1345    
1346    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1347    
1348            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1349            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1350            is exactly singular.
1351    
1352    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1353    
1354            * DESCRIPTION (Date): updated -> release 0.9975-6
1355    
1356    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1357    
1358            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1359            now returns symmetric.
1360    
1361            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1362    
1363            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1364            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1365    
1366            * R/Auxiliaries.R (.type.kind): added
1367    
1368    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1369    
1370            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1371            running src/CSparse_install.sh
1372    
1373            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1374    
1375    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1376    
1377            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1378            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1379    
1380            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1381    
1382            * tests/Class+Meth.R (tstMatrixClass): now assure
1383            the (important in method programming) property :
1384    
1385                    ###>>  Every "Matrix" is either
1386                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1387    
1388                    (where "*" stands for "Matrix")
1389    
1390            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1391    
1392            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1393            * tests/validObj.R: checks for "comparison"
1394    
1395            * R/sparseMatrix.R ([): improved indexing for sparse;
1396                    trying to keep <symmetric>[ n, n] symmmetric
1397    
1398            * tests/indexing.R: indexing for logical sparse now ok
1399    
1400    
1401    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1402    
1403            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1404    
1405            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1406    
1407    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1408    
1409            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1410    
1411            * tests/simple.R: validObject() checking the above.
1412    
1413            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1414            replacing both dgCMatrix_validate and lgCM*.
1415    
1416            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1417            fix dimnames setting in other places.
1418            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1419    
1420    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1421    
1422            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1423    
1424            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1425            symmetry test, via
1426            * R/Auxiliaries.R (.as.dgC.0.factors):
1427    
1428    2006-11-01  Douglas Bates  <bates@r-project.org>
1429    
1430            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1431            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1432            <CsparseMatrix>) added
1433    
1434    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1435    
1436            * tests/matprod.R: add a variation of Harri's example
1437    
1438            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1439            recursive infinitely.
1440    
1441            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1442    
1443            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1444    
1445    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1446    
1447            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1448            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1449            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1450            satisfy the above test.
1451    
1452    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1453    
1454            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1455    
1456            * R/dgCMatrix.R: solve(a, b="missing") based on
1457            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1458            RHS = NULL.
1459    
1460            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1461            add more (needed) [t]crossprod() methods.
1462    
1463            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1464    
1465            * R/Auxiliaries.R (as_CspClass): cleanup
1466            (drop0): internal utility for "Csparse_drop(*, 0)"
1467            (.bail.out.2): encourage active feedback
1468    
1469    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1470    
1471            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1472    
1473            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1474            non-valid or 'sorted' case).
1475    
1476            * R/dsparseMatrix.R: add "chol" method.
1477            * R/ddenseMatrix.R: ditto
1478    
1479            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1480            * NAMESPACE (Ops)
1481            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1482            coercion; deprecating direct lower level coercions.
1483    
1484            * R/*.R (seq): use seq_len() and seq_along() where possible.
1485    
1486    
1487    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1488    
1489            * DESCRIPTION (Version): 0.9975-5 ready for release
1490    
1491    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1492    
1493            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1494    
1495    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1496    
1497            * R/AllClass.R (corMatrix): add 'validity' check;
1498                    comment out unused "LDL" class definition
1499            * NAMESPACE: mention, but do not export "LDL" class
1500            * R/corMatrix.R: new (simple), needed for R-devel with
1501            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1502              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1503    
1504    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1505    
1506            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1507            use Rprintf and R's error handling.
1508    
1509    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1510    
1511            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1512            * tests/matprod.R: add tests for the bug fixed.
1513    
1514    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1515    
1516            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1517            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1518    
1519    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1520    
1521            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1522    
1523    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1524    
1525            * DESCRIPTION (Version): 0.9975-3
1526    
1527            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1528            (sparse) matrices.
1529            * man/bdiag.Rd: docu + examples
1530    
1531            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1532    
1533            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1534            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1535    
1536            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1537            that result is sparse or diagonal (and not dense).
1538    
1539            * man/Subassign-methods.Rd: fix examples
1540    
1541            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1542            should always return a sparse (and not sometimes a diagonal) matrix.
1543    
1544    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1545    
1546            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1547    
1548    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1549    
1550            * DESCRIPTION (Version): 0.9975-2
1551    
1552            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1553    
1554    2006-10-02  Douglas Bates  <bates@R-project.org>
1555    
1556            * tests/dg_Matrix.R: Simplify test taking into account new code.
1557    
1558    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1559    
1560            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1561    
1562            * R/lsTMatrix.R: new files w/ missing methods
1563            * R/nsTMatrix.R:  "  'for completeness'
1564    
1565            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1566    
1567            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1568    
1569    
1570    2006-09-28  Douglas Bates  <bates@R-project.org>
1571    
1572            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1573            included.
1574    
1575            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1576            Export C-callable functions used in Zt_create in lme4.
1577    
1578    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1579    
1580            * DESCRIPTION (Version): 0.9975-1
1581    
1582            * tests/simple.R: less checks fail; using NA, found that our
1583                    kronecker() is not base-compatible with NA's.
1584    
1585            * R/dMatrix.R: "Compare" method now implemented for all cases
1586    
1587            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1588    
1589            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1590    
1591            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1592            * src/dspMatrix.c (dspMatrix_validate): ditto
1593    
1594            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1595              including coercion to [nl]tTMatrix.
1596    
1597            * R/diagMatrix.R (show): print a header line as for other classes.
1598    
1599    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1600    
1601            * src/Makefile.win (SUBDIRS): fix typo
1602    
1603    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1604    
1605            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1606    
1607    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1608    
1609            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1610            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1611            accept a symmetric matrix).
1612            * tests/group-methods.R: Uncomment test of crossprod applied to
1613            lsCMatrix objects.
1614    
1615    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1616    
1617            * R/AllClass.R (symmetricMatrix): add validity method (available
1618            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1619    
1620            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1621    
1622            * tests/indexing.Rout.save:
1623            * tests/indexing.R: additions, mainly for 'lsparse'
1624    
1625            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1626            case.
1627    
1628            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1629    
1630    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1631    
1632            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1633                    as 'N' (1-letter - Ok?)
1634    
1635            * tests/group-methods.R: add test for logical + NAs
1636    
1637            * R/dMatrix.R ("Compare"): fix to work with NA's
1638    
1639            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1640    
1641            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1642                    which is implemented.
1643    
1644    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1645    
1646            * src/chm_common.c: coerce logical <-> double instead of
1647            typecasting;  needed for "l" matrix handling in cholmod.
1648    
1649            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1650    
1651            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1652            (Tsp2grNEL): other fixes needed
1653    
1654    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1655    
1656            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1657                    Matrices, since "lMatrix", also "lsparseM" can have NA
1658            * R/ndenseMatrix.R, etc: new source files
1659            * man/nsparseMatrix-classes.Rd, etc: new help files
1660            * tests/: adaptions
1661            * src/chm_common.c (chm_dense_to_SEXP): and others:
1662                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1663            * src/Csparse.c, etc: ditto
1664    
1665    2006-09-11  Douglas Bates  <bates@R-project.org>
1666    
1667            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1668            alloc_d**Matrix functions to the lme4 package.
1669    
1670    2006-09-09  Douglas Bates  <bates@R-project.org>
1671    
1672            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1673            fixed
1674    
1675    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1676    
1677            * R/lMatrix.R: new
1678    
1679            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1680    
1681            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1682            * man/tcrossprod.Rd: ditto
1683    
1684    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1685    
1686            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1687            for exported functions
1688            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1689            Remove partitioning algorithms for sparse matrix reordering.  The
1690            copyright on the Metis code was problematic and the methods were
1691            rarely used.
1692            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1693            operations are now done entirely in CHOLMOD code.
1694    
1695    2006-09-06  Douglas Bates  <bates@R-project.org>
1696    
1697            * src/Mutils.h: Remove functions that are no longer used.
1698    
1699    2006-09-04  Douglas Bates  <bates@R-project.org>
1700    
1701            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1702            * src/DEPS.mkf: update
1703    
1704    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1705    
1706            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1707            * DESCRIPTION (Version): 0.9975-0
1708            (Depends): R (>= 2.4.0)
1709    
1710    2006-09-01  Douglas Bates  <bates@R-project.org>
1711    
1712            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1713    
1714    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1715    
1716            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1717            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1718    
1719            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1720    
1721    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1722    
1723            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1724            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1725            * R/dsparseMatrix.R: ditto
1726            * R/Csparse.R: ditto
1727    
1728    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1729    
1730            * R/dMatrix.R (Compare): improve availability of "<", etc
1731            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1732    
1733    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1734    
1735            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1736            of a 0-index which was used as 1-index (..hmm)
1737    
1738            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1739    
1740            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1741            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1742            (.is.diagonal): ditto
1743    
1744            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1745    
1746            * R/Matrix.R (Matrix): also work for NA data
1747    
1748  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1749    
1750          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting

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