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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 2248, Tue Aug 26 15:34:16 2008 UTC
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1    2008-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dgCMatrix.c (dgCMatrix_LU): partially revert change
4            r2175 (2008-04-23) and do give an error for a singular matrix.
5            * man/lu.Rd, R/Auxiliaries.R (detSparseLU): adapt to that.
6    
7            * R/LU.R: expand( <sparseLU> )
8    
9            * NAMESPACE, man/all.equal-methods.Rd:
10            * R/Matrix.R (all.equal): methods for Matrices,
11            * R/sparseMatrix.R, R/sparseVector.R: sparseMatrices and -Vectors
12    
13    
14    2008-08-23  Douglas Bates <bates@stat.wisc.edu>
15    
16            * [r2243] R/CHMfactor.R, man/CHMfactor-class.Rd: Added expand method and
17              documentation for CHMfactor class
18            * [r2241] R/CHMfactor.R: Added trivial coercion method for CHMfactor ->
19              pMatrix
20    
21    2008-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/nsCMatrix.R (setAs(., dgTMatrix))): remove unused method
24    
25    2008-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/Ops.R (.Ops2dge.via.x, and many others): eliminate never-used
28            variable assignments {from "next version" codetools}.
29            * R/Csparse.R, R/Tsparse.R: ditto
30    
31    2008-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/sparseVector.R (sp2vec, coerce to sparseVector):
34            make sure no integer overflows happen, and use double precision
35            (n, index) where appropriate.
36    
37            * tests/Simple.R: test "large" sparse vectors.
38    
39    2008-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/AllClass.R (sparseVector): 'length' and 'i' are "numeric", not
42            just integer (allowing much longer length).
43    
44    2008-07-28  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/AllClass.R (diagonalMatrix): extend  "sparseMatrix" instead of
47            "denseMatrix".  This renders "scarceMatrix" dispensable and
48            invalidates part of MM's presentations on "space of Matrix
49            classes", but seems cleaner overall.
50    
51            * R/diagMatrix.R, etc: eliminate "scarceMatrix", replacing it by
52            "sparseMatrix" in method signatures;
53            further, instead of coercing to "sparseMatrix", coerce to
54            "TsparseMatrix" now.
55    
56    2008-07-26  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * src/dgCMatrix.c (dgCMatrix_qrsol): allow third argument 'order' in
59            .Call(.)
60            * R/sparseMatrix.R (lm.fit.sparse), src/dgCMatrix.h, src/init.c: ditto
61    
62    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
65            recursion in new test in
66            * tests/matprod.R: testing the above and another solve() case, below
67    
68            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
69            e.g. triangular 'x'.
70    
71            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
72            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
73            correctly with unit-triangular x
74    
75            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
76            instead of not checking diagU.
77    
78            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
79            experiments where diagonalMatrix would extend sparse*.
80    
81    
82    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
85            "x@p[ncol(x)]" instead of length(x@i).
86            * R/Auxiliaries.R (nnzero): ditto
87    
88            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
89            since that fails for over-allocated i.
90    
91            * tests/validObj.R: more testing of over-allocated (i,x) slots
92    
93    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
96            'sort_in_place' and set it to TRUE in call from
97            * src/Csparse.c (Csparse_validate): sort in place, making sure that
98            validObject() continues sort the columns if needed.
99    
100            * tests/validObj.R: now tests that more thoroughly, and
101            * man/CsparseMatrix-class.Rd: documents it.
102    
103    2008-07-22  Douglas Bates <bates@stat.wisc.edu>
104    
105            * [r2233] src/chm_common.c: sort columns more carefully in
106              as_cholmod_sparse
107            * [r2231] src/chm_common.c: check for sorted columns in
108              as_cholmod_sparse instead of assuming it
109            * [r2228] src/cs_utils.c: Use R_alloc for semi-permanent storage when
110              expanding diagonal
111    
112    
113    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
116            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
117            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
118            diagU2N().
119    
120            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
121            .spDiagonal() and new .trDiagonal().
122    
123            * R/dtCMatrix.R (solve): make use of .trDiagonal()
124    
125    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
128            stumbled upon by Michael H.
129    
130            * tests/validObj.R: testing the bug-fix
131    
132            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
133            versions.
134    
135            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
136            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
137    
138            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
139              AS_CHM_SP() which includes diagU2N.
140    
141            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
142            adapt to 3 arguments.
143    
144    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
145    
146            * [r2220] src/dtCMatrix.c: Correct number of columns for rhs in
147              dtCMatrix_sparse_solve
148            * [r2219] src/cs_utils.c: eye->nz should be -1 for compressed column
149              storage
150            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
151              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
152              new solve method
153            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
154              Csparse_diagU2N functionality into Matrix_as_cs
155    
156    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
159    
160    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
161    
162            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
163              argument with default TRUE
164            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
165              Csparse_diagU2N
166            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
167              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
168              parent array; new solve method for signature(a = "dtCMatrix", b =
169              "sparseMatrix")
170    
171    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/diagMatrix.R (.bdiag): also keep result triangular
174    
175    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
176    
177            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
178              messages
179    
180    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
183            symmetric- or nsparse-Matrix, also fixing the bug introduced with
184            the new version (.999375-10).
185    
186            * tests/Simple.R: regression test for the bugs.
187    
188    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/sparseVector.R (spV2M): fix for "isparseVector".
191            Further, fix <diag> -> <sparseVector> coercion
192            (repSpV): add rep(<sparseVector>, .) method
193    
194            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
195            use as.vector(.).
196    
197            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
198    
199            * R/AllClass.R: new (hidden) class union "scarceMatrix"
200            * R/AllClass.R: sparseVector: add prototype
201    
202            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
203            Kasper Kristensen
204    
205    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * tests/other-pkgs.R: add more interesting Matrix -> graph
208    
209    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
212            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
213    
214    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * DESCRIPTION: release 0.999375-10 to CRAN
217    
218            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
219            .bdiag().
220            * man/bdiag.Rd: update, including test.
221    
222    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * tests/Simple.R: add minimal bdiag() checks
225    
226            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
227              factor out the Tsparse - internal computation into new .bdiag()
228    
229    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/nsparseMatrix.R: specific fast all() and any() methods.
232    
233            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
234            when trying to produce too large result.
235    
236            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
237            very large matrices.
238    
239            * R/sparseMatrix.R (printSpMatrix2): new function, used by
240            show(<sparseMatrix>).
241    
242            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
243    
244    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * src/Mutils.c (m_encodeInd, m_encodeInd2):
247            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
248    
249            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
250            big matrices): -> 2nd argument 'di' instead of 'nr' !
251    
252    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/dtCMatrix.R: faster dgC* -> dtC* method
255            * tests/Simple.R: (hence removed "FIXME")
256    
257            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
258            which can be be turned off for possible speed gains.
259    
260    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
263    
264            * R/not.R: fix !<ldiMatrix>
265            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
266    
267            * R/diagMatrix.R (Ops): fix one-off thinko in
268            <diagonal> o <numeric> methods
269    
270            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
271    
272    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
275            * tests/Simple.R: testing the above
276    
277    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
280    
281    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
284            * NAMESPACE (unname): finally exported
285    
286    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Auxiliaries.R (cholMat): possibly keep packed
289    
290            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
291            for R < 2.7.0.
292    
293            * R/Tsparse.R ([): for triangularMatrix, check if result may be
294            triangular.
295            * tests/indexing.R: regression test
296    
297    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
300            * R/Ops.R: more methods, for lMatrix/nMatrix
301    
302    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/expm.R: new file for all expm() methods; notably new ones for
305            diagonal*, triangular*, symmetric* and also simple "matrix".
306    
307    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
310    
311            * inst/test-tools.R (assert.EQ.mat): better message when not equal
312    
313            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
314    
315            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
316            [dl]denseMatrix {identical slots; but more logical method dispatch}
317    
318    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
321    
322            * R/diagMatrix.R (determinant): method
323    
324    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
327    
328            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
329    
330            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
331            its diagonal
332    
333    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
336    
337            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
338    
339            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
340    
341            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
342    
343    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
346    
347            * R/Ops.R (.do.Logic.lsparse): fix NA case
348    
349            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
350    
351            * R/Auxiliaries.R (nnzero): fix special cases, using
352            * R/Auxiliaries.R (indDiag): new utility
353            * R/Auxiliaries.R (indTri): new argument 'diag'
354    
355            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
356    
357    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
360    
361            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
362            ".tCMatrix" triangular matrix.
363    
364            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
365            'clx' can be class *or* class representation.
366            (nnzSparse): new.
367            (non0ind): new 'xtendSymm' argument; used in
368            * R/Ops.R:
369    
370            * R/pMatrix.R: more efficient determinant() method
371    
372    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
375            * [disactivated] NAMESPACE: export(det)
376    
377            * R/diagMatrix.R (mkDiag): new substitute for diag()
378    
379            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
380            (as0, as1): new utility.
381    
382            * R/Csparse.R (diag, band): need diagU2N()
383    
384            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
385    
386            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
387    
388            * R/Ops.R (Compare): fix <nsp> o <nsp> case
389    
390            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
391    
392    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * R/Auxiliaries.R (signPerm): new utility for
395            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
396    
397            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
398            since we have our own error handler (and can use tryCatch() from R).
399    
400    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
403    
404            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
405            when not positive definite.
406    
407            * R/Auxiliaries.R (asTri): new auxiliary
408            (non0.i): make *much* faster for Tsparse with many non-zero
409            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
410    
411            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
412            test-tools.R , see below
413    
414            * R/dMatrix.R: fix "Summary" method: + diagU2N()
415    
416            * NAMESPACE, R/Matrix.R: add mean() method
417    
418    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
421            cold-hot colors; try *changed* default useAbs = FALSE
422            * man/image-methods.Rd:  nice examples
423    
424    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * inst/test-tools.R (checkMatrix): new function for modularizing part
427            of tstMatrixClass() in tests/Class+Meth.R
428    
429            * R/dsCMatrix.R: coercion from "matrix"
430            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
431    
432            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
433            add test for as(matrix(,0,0), <class>)
434    
435    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
438            work as determinant(matrix(,0,0)).
439    
440            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
441            * man/sparseLU-class.Rd: ditto
442    
443            * R/dgCMatrix.R (determinant): method building on lu()
444            * R/sparseMatrix.R, Matrix.R, ...: ditto
445    
446            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
447    
448    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
451            pattern matrices.
452    
453    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * src/dense.c (dense_to_Csparse): all declarations *before*
456            R_CheckStack(); needed e.g. for ancient gcc 2.96.
457    
458    
459    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * DESCRIPTION (Version): 0.999375-9 --- need to release
462            for R-devel (and R 2.7.0 alpha soon).
463    
464            * R/AllClass.R: drop "double" from "atomicVector" class union
465    
466            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
467            * R/dgeMatrix.R: ditto
468    
469            * R/sparseMatrix.R (summary): count NAs
470    
471            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
472    
473    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
474    
475            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
476            order to become compatible to new R 2.7.0 base::rcond().
477    
478    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
479    
480            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
481    
482            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
483    
484            * inst/test-tools.R (isValid): new utility, used much in
485            * tests/simple.R:
486    
487            * man/BunchKaufman-methods.Rd: added too
488    
489    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
490    
491            * R/dsyMatrix.R: add BunchKaufman() methods.
492            * R/dspMatrix.R:
493    
494            * src/init.c: add dsyMatrix_trf
495    
496    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
497    
498            * DESCRIPTION (Version): release 0.999375-7
499            * src/CHMfactor.c (CHMfactor_update): fix
500    
501    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
502    
503            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
504            internal_chm_factor().
505    
506            * R/AllGeneric.R: do *not* define a "chol" generic
507                    (but rather use the implicit one *without* making pivot
508                    part of the signature)
509            * R/*.R: drop the 'pivot' from chol's signature and make
510                    'pivot=FALSE' a default argument of method definitions.
511    
512            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
513            version of Matrix
514    
515    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
516    
517            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
518    
519            * R/sparseMatrix.R (is.na): new simple method
520            * R/denseMatrix.R (is.na): ditto.
521    
522            * R/diagMatrix.R (.symDiagonal): newly exported utility.
523    
524            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
525    
526            * src/UFsparse_download.sh: -->
527            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
528    
529    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
532            functionality; barely tested in
533            * tests/factorizing.R
534    
535            * src/Csparse.c (diag_tC): new functionality to enable faster
536            determinant(<dsCMatrix>, .) in
537            * R/dsCMatrix.R
538    
539    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
540    
541            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
542              src/CHMfactor.c, src/CHMfactor.h,
543              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
544              Log-determinant of the parent matrix from a CHMfactor object as
545              chm_factor_ldetL2; documentation and support
546    
547    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
550    
551    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
554            warning.
555    
556    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
559    
560            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
561              <diagonal> o <sparse_triangular>
562              setAs(., "nMatrix") added.
563    
564            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
565    
566            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
567                    new argument 'checkDense = FALSE'.
568    
569    
570    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
571    
572            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
573            back-permutation of the matrix exponential.
574    
575            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
576    
577            * DESCRIPTION (Date,Version): ready to release 0.999375-5
578    
579            * tests/simple.R: testing diagN2U
580    
581    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
582    
583            * R/Auxiliaries.R (diagN2U): interface to
584    
585            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
586    
587            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
588    
589    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * src/chm_common.c (chm_diagN2U): new utility.
592    
593            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
594            make use of chm_diagN2U() and hence now preserve triangularity and
595            unit-triangularity.
596    
597            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
598    
599    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
602    
603            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
604            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
605    
606            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
607    
608            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
609    
610            * src/chm_common.c (AS_CHM_FINISH): add note about problem
611            for triangular (diag = "U").
612    
613    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
616            * R/bind.R:  .Call(dense_to_Csparse, *)
617    
618    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * R/Matrix.R (Matrix): no longer use coercions to specific classes
621                    (since we are discouraging them in user code).
622    
623            * tests/*.R: also replaces coercions to specific classes by
624            coercions to super classes.
625    
626            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
627    
628    
629    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
632    
633            * src/dense.c (dense_band): generalized from ddense_band
634    
635            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
636              now for "denseMatrix" (instead of just "ddense*"); much
637              simplified setMethod()s for these.
638    
639            * src/dense.c (dense_to_symmetric): generalized from ddense_*
640    
641    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
644            version of as(*, "symmetricMatric").
645    
646            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
647            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
648    
649    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
650    
651            * R/Matrix.R (subset.ij): utility, as first step to faster
652               M [ <ij-matrix> ] indexing.
653    
654            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
655    
656            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
657            for more efficient symmpart() and skewpart() methods.
658    
659            * src/Mutils.c (equal_string_vectors): utility
660    
661            * src/dense.c (ddense_to_symmetric): new function used in
662    
663            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
664    
665            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
666            order to match the generic (and evade .local(..)).
667    
668            * R/dsCMatrix.R: dgC -> dsC: use C code!
669    
670            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
671            as per TODO
672    
673            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
674    
675            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
676    
677    
678    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
681    
682            * R/Auxiliaries.R (non0.i): take out of non0ind
683    
684            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
685            make tril(), triu(), band() work for "matrix" and all "dense*"
686    
687            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
688            * tests/simple.R: test the fix above
689    
690            * R/sparseMatrix.R ([): simplification: no coerce to <general>
691                    before we use as(., <Tsparse>)[...] anyway
692    
693            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
694    
695            * R/triangularMatrix.R (isTriangular): methods for all subclasses
696            instead of "triangularMatrix" -- just to disambiguate
697    
698    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
701            * tests/indexing.R: example that fails above
702    
703    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
706            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
707                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
708    
709            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
710            * src/Tsparse.h, init.c: ditto
711            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
712                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
713            * R/sparseMatrix.R (isTriangular): hence simplified
714    
715    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * R/Ops.R (.Arith.Csparse): new utility factored out of former
718              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
719    
720    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
723    
724            * inst/test-tools.R (isOrthogonal): new function; also file restructured
725    
726    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
727    
728            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
729            coercion to "nMatrix" and "pMatrix"
730    
731            * R/AllClass.R: "Schur" class;  "number" class union
732            * man/number-class.Rd:
733            * man/Schur-class.Rd:
734    
735            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
736            (.simpleSchur): Schur() method for diagonal matrices
737            (.triSchur):    Schur() method for triangular matrices
738            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
739    
740    
741    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
744    
745    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
748                    in order to ensure 'system = *' is not lost;
749                    formals()$system instead of cut&paste.
750            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
751    
752    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * DESCRIPTION (Date): make ready for release --> 0.999375-4
755    
756            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
757    
758    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
761                    and hence does as.vector(.).
762            * man/pMatrix-class.Rd: docs
763            * R/sparseMatrix.R: fix for printing "integer sparse"
764    
765            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
766    
767            * R/Matrix.R and others: use "exact" function argument list for
768                    both "["   : (x, i,j, ..., drop)
769                    and  "[<-" : (x, i,j, ..., value)
770    
771            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
772            * R/Tsparse.R (replTmat):    ditto
773            * R/diagMatrix.R (replDiag): ditto
774            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
775            * tests/indexing.R: testing the above
776    
777    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
778    
779            * R/sparseMatrix.R (cov2cor): method for sparse matrices
780    
781            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
782    
783            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
784    
785            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
786    
787    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
788    
789            * R/Matrix.R: "generic" cov2cor() method
790    
791            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
792                    speed up Q %*% D %*% t(Q)
793            * tests/dpoMatrix.R: test nearPD()
794    
795    2007-12-05  Doug Bates and Martin Maechler
796    
797            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
798            stats::xtabs() allowing to create sparse matrices.
799    
800    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
801    
802            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
803    
804    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
805    
806            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
807    
808    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
809    
810            * R/LU.R: solve() method for "denseLU"
811    
812    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
813    
814            * DESCRIPTION (Version): 0.999375-3 preparing for release
815    
816            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
817    
818            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
819    
820    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
821    
822            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
823              thanks to Kasper Kristensen.
824            * tests/matprod.R: regression test for that.
825    
826    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
827    
828            * [r4778] R/AllGeneric.R: Check R version before defining generics for
829              primitives
830    
831    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
832    
833            * R/denseMatrix.R (rcond): method
834            * R/sparseQR.R (rcond): method, use x or t(x)
835    
836    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
837    
838            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
839            matrices.
840            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
841    
842            * man/rcond.Rd: mention the more general definition, and add
843            example for non-square matrices.
844    
845            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
846    
847    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
848    
849            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
850    
851    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
852    
853            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
854            * tests/indexing.R: add new regression for the above cases.
855    
856    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
857    
858            * src/Mutils.h (__sun): clause for alloca.h on Solaris
859    
860    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
861    
862            * DESCRIPTION (Date, Version): 0.999375-2
863    
864    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
865    
866            * R/HBMM.R (readMM): make work for pattern matrices as well
867    
868    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
869    
870            * [r4730] src/Mutils.h: declare alloca
871            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
872              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
873              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
874              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
875              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
876              methods; switch writeMM to use CHOLMOD code; repair readMM
877    
878    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
881            Oehlschlaegel's ... result type still to be discussed!
882    
883    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
884    
885            * man/image-methods.Rd: new, combining all image() methods
886    
887    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
888    
889            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
890            to work via dgC...
891    
892            * R/Matrix.R (Matrix): special treatment for "table" (S3)
893    
894    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
895    
896            * R/dgTMatrix.R (image): change defaults to
897                    aspect = "iso", colorkey = FALSE
898    
899    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
900    
901            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
902            must copy its *expanded* x slot before LAPACK call.
903    
904            * tests/matprod.R: test the last days' changes.
905    
906    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
907    
908            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
909              as well as in sources
910            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
911              Lapack call
912    
913    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
914    
915            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
916                    ("Matrix", "matrix") which is needed in some cases.
917            Ditto for solve().
918    
919            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
920            infinite recursion in dispatch for some cases.
921    
922    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
923    
924            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
925              so pointers match
926    
927    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
928    
929            * DESCRIPTION (Date): set ready for release -- 0.999375-1
930    
931    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
932    
933            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
934              src/chm_common.c, src/chm_common.h: Change API for
935              numeric_as_chm_dense and N_AS_CHM_DN
936    
937    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
938    
939            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
940            * tests/matprod.R: regr.test for it
941    
942    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
943    
944            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
945            * tests/group-methods.R: and regression-test it
946    
947    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
948    
949            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
950              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
951              triplet_to_sparse, documentation, use typedefs
952    
953    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
954    
955            * man/dpoMatrix-class.Rd: added 'corMatrix' example
956    
957            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
958            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
959            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
960    
961            * R/lsparseMatrix.R: bug fix in "all" method
962            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
963    
964            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
965            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
966                    + matrix |-> nMatrix coercion
967            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
968            * man/pMatrix-class.Rd: ditto
969    
970            * R/Matrix.R (Summary): method for non-dMatrix
971    
972            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
973            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
974                    test all Summary methods.
975    
976    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
977    
978            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
979    
980    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
981    
982            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
983    
984            * R/pMatrix.R (t?crossprod): methods for pMatrix
985    
986    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
987    
988            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
989    
990    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
991    
992            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
993              trying to fix a subtle bug - which has been somewhere else.
994    
995    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
996    
997            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
998              solve the bug
999    
1000    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1001    
1002            * src/dgCMatrix.c (compressed_to_TMatrix):
1003    
1004    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1005    
1006            * src/Csparse.c (Rsparse_validate): new, to have some validity
1007            checking for RsparseMatrix
1008            * src/dgCMatrix.c (xRMatrix_validate): ditto
1009            * src/dtCMatrix.c (tRMatrix_validate): ditto
1010    
1011    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
1012    
1013            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
1014              lgRMatrix
1015            * [r4568] DESCRIPTION: Prepare for bug-fix release
1016            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
1017              for declaration of cholmod_symmetry
1018    
1019    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
1021            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
1022            release.
1023    
1024    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
1025    
1026            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
1027              functions - no longer used
1028            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
1029              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
1030              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
1031              Alloca
1032    
1033    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
1034    
1035            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
1036              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
1037              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
1038              src/t_gCMatrix_colSums.c: more R_CheckStack()s
1039    
1040    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
1041    
1042            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
1043              the required amount of memory then call M_numeric_as_chm_dense.
1044            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
1045              (like Calloc but calling alloca)
1046    
1047    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1048    
1049            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
1050            and extended with more sophisticated 'col.names' option.
1051            * NAMESPACE: export  printSparseMatrix()
1052            * man/printSpMatrix.Rd: document, incl. examples
1053    
1054    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
1055    
1056            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
1057              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
1058              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
1059    
1060    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1061    
1062            * DESCRIPTION (Version): 0.99875-4
1063    
1064            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
1065            some dimnames perservation.
1066    
1067            * R/dsTMatrix.R (t-method): keep dimnames
1068            * R/dtTMatrix.R:  ditto
1069    
1070            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
1071            and ncol(.) < 10
1072    
1073            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
1074            from Mutils.h
1075    
1076            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
1077            e.g. in as(<ngCMatrix>, "matrix")
1078    
1079    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
1080    
1081            * [r4529] .: Create a branch for the API changes from the 0.99875
1082              series to the 0.999375 series
1083            * [r4530] DESCRIPTION, inst/include/Matrix.h,
1084              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
1085              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
1086              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
1087              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
1088              as_cholmod_x functions
1089    
1090    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
1091    
1092            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
1093              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
1094              to Comparisons
1095    
1096    >>>>>>> .merge-right.r4561
1097    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1098    
1099            * DESCRIPTION (Version): 0.99875-3 ready to be released.
1100    
1101            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
1102    
1103            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
1104            that should also work in a future version of R.
1105    
1106    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1107    
1108            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
1109    
1110            * R/sparseVector.R: more *sparseVector coercions, notably for
1111            non - double ones.
1112    
1113    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1114    
1115            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
1116              notably the new ones building on the new .Call(.)s:
1117    
1118            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
1119            all 4 of [dlin]gCMatrix_colSums().
1120    
1121    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
1122    
1123            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
1124            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
1125              result
1126    
1127    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1128    
1129            * R/kronecker.R: fix typo (could lead to inf.recursion)
1130            * test/simple.R: testing that
1131    
1132            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
1133            method as well (which can have arguments, show() can't).
1134    
1135    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
1136    
1137            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
1138              added dgCMatrix_colSums for [col,row][Sums,Means]
1139    
1140    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
1141    
1142            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
1143              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
1144              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
1145            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
1146              class
1147            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
1148              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
1149              row names to store the levels - duh!  Added an example.
1150    
1151    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1152    
1153            * src/Csparse.c (Csparse_validate): check for *repeated* entries
1154            thanks to example from Christian Buchta; with a test here:
1155            * tests/simple.R:
1156    
1157    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1158    
1159            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
1160            of colSums(*, sparseResult = TRUE)
1161    
1162    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1163    
1164            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
1165            'na.rm = FALSE' as "everywhere" else in R.
1166    
1167    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
1168    
1169            * [r4421] src/CSparse_install.sh: Modify for new organization of
1170              CSparse package
1171            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
1172              SuiteSparse
1173            * [r4426] src/Makefile: add ./UFconfig to the include path for
1174              compilation
1175            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
1176            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
1177              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
1178    
1179    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1180    
1181            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
1182            * R/sparseMatrix.R (prSpMatrix): now gives a message about
1183            suppressed column names.
1184    
1185    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
1186    
1187            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
1188              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
1189              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
1190              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
1191              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
1192              Remove warnings after change to const char* CHAR
1193    
1194    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
1195    
1196            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
1197              type of M_cholmod_ssmult
1198    
1199    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
1200    
1201            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
1202              src/init.c: Yet another cholmod export - cholmod_ssmult
1203    
1204    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1205    
1206            * NAMESPACE: exported drop0(), since
1207            * man/drop0.Rd: I have seen several cases, I really wanted to use
1208            it, so our users may want too.
1209    
1210    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1211    
1212            * man/colSums.Rd: separately document colSums() etc, since these
1213            have the extra argument 'sparseResult'.
1214    
1215    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1216    
1217            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
1218            * man/spMatrix.Rd: docu., including examples
1219    
1220            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
1221            in order to make colMeans() etc fast *and* correct.
1222            * R/sparseVector.R (replSPvec): "[<-" functionality for
1223            sparseVectors; tested in
1224            * tests/simple.R:
1225    
1226    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1227    
1228            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1229            (very) sparse Matrices; output similar to Matlab's print().
1230    
1231    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
1232    
1233            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
1234            0-based, indices (Jose Quesada <quesada@gmail.com>).
1235    
1236    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
1237    
1238            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
1239    
1240    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1241    
1242            * R/Auxiliaries.R (sparsapply): new utility, much faster than
1243            tapply1() for large sparse matrices.
1244    
1245    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1246    
1247            * R/Matrix.R (dim<-): reshape now via sparseVector.
1248    
1249            * R/sparseVector.R: methods and function for
1250            * R/AllClass.R: new "sparseVector" class and daughters.
1251            * NAMESPACE: export new classes
1252    
1253    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1254    
1255            * DESCRIPTION (Version): 0.99875-1
1256            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1257    
1258    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1259    
1260            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1261            indexing
1262            * tests/indexing.R: test set for that.
1263    
1264    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1265    
1266            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1267            entries.
1268            * tests/indexing.R(out): add regression test for it
1269    
1270    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1271    
1272            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1273            name for "!" method definitions.
1274    
1275    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1276    
1277            * R/Tsparse.R (intI): new utility, used for "[" :
1278                    Cleanup up there, and fixes for duplicated indices - more TODO!
1279    
1280            * tests/indexing.R(out): more tests
1281    
1282    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1283    
1284            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1285            code that is now part of the R Lapack library.
1286    
1287            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1288            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1289    
1290    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1291    
1292            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1293    
1294    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1295    
1296            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1297            up with extraneous names '0'...'<n-1>'
1298    
1299    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1300    
1301            * R/dgTMatrix.R (mat2dgT): care about NAs
1302    
1303    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1304    
1305            * R/kronecker.R: triangularity preserving methods
1306    
1307    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1308    
1309            * R/kronecker.R: new file collecting kronecker() methods in one
1310                    place.  Goal: become much faster!
1311    
1312    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1313    
1314            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1315            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1316            can be much faster.
1317    
1318            * tests/matprod.R: add regression tests for these (upper & lower).
1319    
1320    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1321    
1322            * R/Matrix.R (diff): method for our Matrices.
1323    
1324            * R/sparseMatrix.R (isDiagonal): check dim()!
1325    
1326    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1327    
1328            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1329            proposal from Tamas Papp.
1330    
1331    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1332    
1333            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1334    
1335            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1336            rather define and export  cBind() and rBind() only.
1337            --> useRs *must* change code that used to have cbind()/rbind() !!
1338    
1339            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1340            * R/bind.Rout.save: ditto
1341    
1342    2007-02-16  Douglas Bates  <bates@r-project.org>
1343    
1344            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1345            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1346            const modifier on declaration of the array 'valid'
1347    
1348    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1349    
1350            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1351    
1352    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1353    
1354            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1355    
1356            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1357            * tests/simple.R: test the above and some of these coercions:
1358    
1359            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1360                    be careful to avoid infinite recursion, using new coercions in
1361            * R/ngCMatrix.R and nsC... and ntC...
1362            * R/lsparseMatrix.R: ditto
1363    
1364            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1365    
1366            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1367            * R/Rsparse.R: reactivate .Call()s
1368    
1369            * tests/Class+Meth.R: a bit more on actual classes
1370    
1371    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1372    
1373            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1374    
1375    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1376    
1377            * DESCRIPTION (Version): 0.9975-10 to upload
1378    
1379            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1380            specific classes less unconditionally.
1381    
1382            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1383    
1384            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1385    
1386            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1387            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1388            R_to_CMatrix segfaults on one platform.
1389            Eliminate most coercion method to *specific* classes, and replace
1390            with virtual classes coercions.
1391    
1392    
1393    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1394    
1395            * src/init.c: export the CHM...._validate() placeholders, since
1396            they *are* called.
1397    
1398            * tests/Class+Meth.R (classCanCoerce): and starting to test
1399            all as(<from>, <to>)
1400    
1401    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1402    
1403            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1404            * tests/indexing.R: tested now
1405            * tests/indexing.Rout.save: updated
1406    
1407            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1408            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1409            appropriate.
1410    
1411            * NAMESPACE: export a trivial
1412            * R/Matrix.R: drop() Matrix-method
1413    
1414            * R/AllClass.R: moved all prototypes to virtual super classes.
1415    
1416            * R/Rsparse.R: many more coercions to have less exceptions in
1417            * tests/Class+Meth.R:
1418    
1419            * R/Ops.R (Compare): tweak for case with NA
1420            * tests/simpl.R: hence another 'FIXME' eliminated
1421    
1422    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1423    
1424            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1425            objects.
1426    
1427            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1428              and more of "!", "&", "|", all, any; coercions
1429    
1430            * R/Rsparse.R: many coercions (which enable quite a few other
1431            methods), thanks to enhancements in
1432            * src/dgCMatrix.c (R_to_CMatrix): new, and
1433            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1434            symmetric & triangular and ..RMatrix objects.
1435    
1436            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1437            renamed file from src/dsTMatrix.c;
1438            now dealing with symmetric and triangular Tsparse coercions, both
1439            to dense and general.
1440    
1441    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1442    
1443            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1444    
1445            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1446            where sensible when the <numeric> is of length > 1.
1447    
1448    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1449    
1450            * R/Matrix.R ([<-): for M[] <- value: fix length
1451    
1452    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1453    
1454            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1455            * R/ndenseMatrix.R: new coercions n* -> l*
1456    
1457    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1458    
1459            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1460    
1461            * R/Ops.R ("Logic"): and other "Ops", many updates
1462    
1463    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1464    
1465            * src/Mutils.h (SET_DimNames): new utility
1466    
1467            * R/Auxiliaries.R (nnzero): improved and now exported via
1468    
1469            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1470    
1471    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1472    
1473            * R/diagMatrix.R (!): fix typo.
1474    
1475    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1476    
1477            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1478                    allow to pass class definition --> speedup
1479            * R/sparseMatrix.R: apply the above
1480    
1481            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1482    
1483            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1484            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1485            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1486    
1487            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1488    
1489            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1490            and use it for "sparse*" as well, since it's faster than the
1491            as_Csparse(.) way.
1492    
1493    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1494    
1495            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1496    
1497    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1498    
1499            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1500            as method for   M[ ij ] <- v
1501            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1502    
1503            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1504            FALSE answer
1505    
1506            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1507            * tests/indexing.R: test it, and some of the above
1508    
1509    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1510    
1511            * R/Auxiliaries.R (is_duplicatedT): new utility
1512    
1513    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1514    
1515            * src/init.c (R_init_Matrix): export cholmod_scale
1516    
1517    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1518    
1519            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1520            base::as.matrix to (x, ...)
1521    
1522    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1523    
1524            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1525            file; start using "Logic", hence
1526    
1527            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1528            * NAMESPACE: import and export "Logic"
1529    
1530    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1531    
1532            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1533            only needed previously to R version 2.5.0.
1534    
1535    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1536    
1537            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1538    
1539            * R/Tsparse.R (replTmat): fix subassignment of triangular
1540            * R/Csparse.R (replCmat): ditto
1541            * tests/indexing.R: more tests, incl the above fix
1542    
1543    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1544    
1545            * R/Auxiliaries.R (drop0): extend for non CSparse
1546            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1547    
1548            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1549                    use uplo correctly (!); other places: use uplo_P() macro
1550    
1551            * R/Csparse.R (replCmat): call diagU2N() when needed
1552            * R/Tsparse.R (replTmat): ditto
1553    
1554            * src/dtCMatrix.c (tCMatrix_validate): new
1555            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1556            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1557    
1558            * R/diagMatrix.R (replDiag): to use in [<-
1559    
1560    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1561    
1562            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1563                    also more general diagU2N().
1564    
1565    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1566    
1567            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1568            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1569    
1570    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1571    
1572            * tests/bind.R: a few more cases
1573            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1574    
1575            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1576            * R/ddenseMatrix.R (cbind2/rbind2)
1577            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1578            * tests/indexing.R
1579            * tests/indexing.Rout.save: updated
1580    
1581    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1582    
1583            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1584            * tests/indexing.R
1585    
1586    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1587    
1588            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1589            align with proper position of "0", i.e., right for integers.
1590            argument 'align' by default is "fancy".
1591    
1592    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1593    
1594            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1595            * R/Csparse.R: and fix "Compare" for more cases.
1596            * tests/Class+Meth.R: test some of these (m == m, m != m)
1597    
1598    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1599    
1600            * R/lsparseMatrix.R: all() and any() methods
1601            * R/ldenseMatrix.R:      ditto
1602            * NAMESPACE, R/Matrix.R: ditto
1603    
1604            * man/all-methods.Rd: document them minimally
1605    
1606            * tests/simple.R: add a few examples for these
1607    
1608    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1609    
1610            * R/Tsparse.R ([): fix long standing typo in symmetric case
1611            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1612    
1613    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1614    
1615            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1616            to LL before converting to a sparse matrix. (The LDL form can be
1617            converted to a sparse matrix but it is implicitly a unit
1618            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1619    
1620    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1621    
1622            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1623    
1624    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1625    
1626            * DESCRIPTION (Version): updated -> release 0.9975-7
1627            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1628    
1629    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1630    
1631            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1632    
1633    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1634    
1635            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1636            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1637            is exactly singular.
1638    
1639    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1640    
1641            * DESCRIPTION (Date): updated -> release 0.9975-6
1642    
1643    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1644    
1645            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1646            now returns symmetric.
1647    
1648            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1649    
1650            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1651            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1652    
1653            * R/Auxiliaries.R (.type.kind): added
1654    
1655    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1656    
1657            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1658            running src/CSparse_install.sh
1659    
1660            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1661    
1662    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1663    
1664            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1665            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1666    
1667            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1668    
1669            * tests/Class+Meth.R (tstMatrixClass): now assure
1670            the (important in method programming) property :
1671    
1672                    ###>>  Every "Matrix" is either
1673                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1674    
1675                    (where "*" stands for "Matrix")
1676    
1677            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1678    
1679            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1680            * tests/validObj.R: checks for "comparison"
1681    
1682            * R/sparseMatrix.R ([): improved indexing for sparse;
1683                    trying to keep <symmetric>[ n, n] symmmetric
1684    
1685            * tests/indexing.R: indexing for logical sparse now ok
1686    
1687    
1688    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1689    
1690            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1691    
1692            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1693    
1694    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1695    
1696            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1697    
1698            * tests/simple.R: validObject() checking the above.
1699    
1700            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1701            replacing both dgCMatrix_validate and lgCM*.
1702    
1703            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1704            fix dimnames setting in other places.
1705            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1706    
1707    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1708    
1709            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1710    
1711            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1712            symmetry test, via
1713            * R/Auxiliaries.R (.as.dgC.0.factors):
1714    
1715    2006-11-01  Douglas Bates  <bates@r-project.org>
1716    
1717            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1718            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1719            <CsparseMatrix>) added
1720    
1721    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1722    
1723            * tests/matprod.R: add a variation of Harri's example
1724    
1725            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1726            recursive infinitely.
1727    
1728            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1729    
1730            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1731    
1732    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1733    
1734            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1735            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1736            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1737            satisfy the above test.
1738    
1739    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1740    
1741            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1742    
1743            * R/dgCMatrix.R: solve(a, b="missing") based on
1744            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1745            RHS = NULL.
1746    
1747            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1748            add more (needed) [t]crossprod() methods.
1749    
1750            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1751    
1752            * R/Auxiliaries.R (as_CspClass): cleanup
1753            (drop0): internal utility for "Csparse_drop(*, 0)"
1754            (.bail.out.2): encourage active feedback
1755    
1756    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1757    
1758            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1759    
1760            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1761            non-valid or 'sorted' case).
1762    
1763            * R/dsparseMatrix.R: add "chol" method.
1764            * R/ddenseMatrix.R: ditto
1765    
1766            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1767            * NAMESPACE (Ops)
1768            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1769            coercion; deprecating direct lower level coercions.
1770    
1771            * R/*.R (seq): use seq_len() and seq_along() where possible.
1772    
1773    
1774    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1775    
1776            * DESCRIPTION (Version): 0.9975-5 ready for release
1777    
1778    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1779    
1780            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1781    
1782    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1783    
1784            * R/AllClass.R (corMatrix): add 'validity' check;
1785                    comment out unused "LDL" class definition
1786            * NAMESPACE: mention, but do not export "LDL" class
1787            * R/corMatrix.R: new (simple), needed for R-devel with
1788            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1789              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1790    
1791    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1792    
1793            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1794            use Rprintf and R's error handling.
1795    
1796    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1797    
1798            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1799            * tests/matprod.R: add tests for the bug fixed.
1800    
1801    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1802    
1803            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1804            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1805    
1806    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1807    
1808            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1809    
1810    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1811    
1812            * DESCRIPTION (Version): 0.9975-3
1813    
1814            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1815            (sparse) matrices.
1816            * man/bdiag.Rd: docu + examples
1817    
1818            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1819    
1820            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1821            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1822    
1823            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1824            that result is sparse or diagonal (and not dense).
1825    
1826            * man/Subassign-methods.Rd: fix examples
1827    
1828            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1829            should always return a sparse (and not sometimes a diagonal) matrix.
1830    
1831    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1832    
1833            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1834    
1835    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1836    
1837            * DESCRIPTION (Version): 0.9975-2
1838    
1839            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1840    
1841    2006-10-02  Douglas Bates  <bates@R-project.org>
1842    
1843            * tests/dg_Matrix.R: Simplify test taking into account new code.
1844    
1845    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1846    
1847            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1848    
1849            * R/lsTMatrix.R: new files w/ missing methods
1850            * R/nsTMatrix.R:  "  'for completeness'
1851    
1852            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1853    
1854            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1855    
1856    
1857    2006-09-28  Douglas Bates  <bates@R-project.org>
1858    
1859            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1860            included.
1861    
1862            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1863            Export C-callable functions used in Zt_create in lme4.
1864    
1865    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1866    
1867            * DESCRIPTION (Version): 0.9975-1
1868    
1869            * tests/simple.R: less checks fail; using NA, found that our
1870                    kronecker() is not base-compatible with NA's.
1871    
1872            * R/dMatrix.R: "Compare" method now implemented for all cases
1873    
1874            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1875    
1876            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1877    
1878            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1879            * src/dspMatrix.c (dspMatrix_validate): ditto
1880    
1881            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1882              including coercion to [nl]tTMatrix.
1883    
1884            * R/diagMatrix.R (show): print a header line as for other classes.
1885    
1886    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1887    
1888            * src/Makefile.win (SUBDIRS): fix typo
1889    
1890    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1891    
1892            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1893    
1894    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1895    
1896            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1897            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1898            accept a symmetric matrix).
1899            * tests/group-methods.R: Uncomment test of crossprod applied to
1900            lsCMatrix objects.
1901    
1902    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1903    
1904            * R/AllClass.R (symmetricMatrix): add validity method (available
1905            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1906    
1907            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1908    
1909            * tests/indexing.Rout.save:
1910            * tests/indexing.R: additions, mainly for 'lsparse'
1911    
1912            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1913            case.
1914    
1915            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1916    
1917    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1918    
1919            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1920                    as 'N' (1-letter - Ok?)
1921    
1922            * tests/group-methods.R: add test for logical + NAs
1923    
1924            * R/dMatrix.R ("Compare"): fix to work with NA's
1925    
1926            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1927    
1928            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1929                    which is implemented.
1930    
1931    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1932    
1933            * src/chm_common.c: coerce logical <-> double instead of
1934            typecasting;  needed for "l" matrix handling in cholmod.
1935    
1936            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1937    
1938            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1939            (Tsp2grNEL): other fixes needed
1940    
1941    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1942    
1943            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1944                    Matrices, since "lMatrix", also "lsparseM" can have NA
1945            * R/ndenseMatrix.R, etc: new source files
1946            * man/nsparseMatrix-classes.Rd, etc: new help files
1947            * tests/: adaptions
1948            * src/chm_common.c (chm_dense_to_SEXP): and others:
1949                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1950            * src/Csparse.c, etc: ditto
1951    
1952    2006-09-11  Douglas Bates  <bates@R-project.org>
1953    
1954            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1955            alloc_d**Matrix functions to the lme4 package.
1956    
1957    2006-09-09  Douglas Bates  <bates@R-project.org>
1958    
1959            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1960            fixed
1961    
1962    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1963    
1964            * R/lMatrix.R: new
1965    
1966            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1967    
1968            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1969            * man/tcrossprod.Rd: ditto
1970    
1971    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1972    
1973            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1974            for exported functions
1975            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1976            Remove partitioning algorithms for sparse matrix reordering.  The
1977            copyright on the Metis code was problematic and the methods were
1978            rarely used.
1979            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1980            operations are now done entirely in CHOLMOD code.
1981    
1982    2006-09-06  Douglas Bates  <bates@R-project.org>
1983    
1984            * src/Mutils.h: Remove functions that are no longer used.
1985    
1986    2006-09-04  Douglas Bates  <bates@R-project.org>
1987    
1988            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1989            * src/DEPS.mkf: update
1990    
1991    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1992    
1993            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1994            * DESCRIPTION (Version): 0.9975-0
1995            (Depends): R (>= 2.4.0)
1996    
1997    2006-09-01  Douglas Bates  <bates@R-project.org>
1998    
1999            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
2000    
2001    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
2002    
2003            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
2004            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
2005    
2006            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
2007    
2008    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
2009    
2010            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
2011            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
2012            * R/dsparseMatrix.R: ditto
2013            * R/Csparse.R: ditto
2014    
2015    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
2016    
2017            * R/dMatrix.R (Compare): improve availability of "<", etc
2018            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
2019    
2020    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2021    
2022            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
2023            of a 0-index which was used as 1-index (..hmm)
2024    
2025            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
2026    
2027            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
2028            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
2029            (.is.diagonal): ditto
2030    
2031            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
2032    
2033            * R/Matrix.R (Matrix): also work for NA data
2034    
2035  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2036    
2037          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting

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