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revision 2159, Sat Mar 29 08:09:05 2008 UTC revision 2255, Sat Aug 30 07:20:33 2008 UTC
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1    2008-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.999375-13 released to CRAN
4    
5    2008-08-29  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Auxiliaries.R (attrSlotNames, attrSlots, attr.all_Mat): new
8            utilities, for now to be used in all.equal() methods.
9    
10            * R/Matrix.R (all.equal_Mat): be more careful (less tolerant) in
11            all.equal() methods.
12            * R/sparseMatrix.R: ditto
13    
14    2008-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * DESCRIPTION (Version): 0.999375-12 released to CRAN
17    
18            * R/Ops.R (Compare(<Csparse>,<Csparse>): fix for nsparseMatrix
19    
20    2008-08-27  Douglas Bates <bates@stat.wisc.edu>
21    
22            * R/sparseMatrix.R: fac2sparse() for NA's
23    
24    2008-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/sparseVector.R (all.equal.sparseV): make work for nsparseVector's
27    
28    2008-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * src/dgCMatrix.c (dgCMatrix_LU): partially revert change
31            r2175 (2008-04-23) and do give an error for a singular matrix.
32            * man/lu.Rd, R/Auxiliaries.R (detSparseLU): adapt to that.
33    
34            * R/LU.R: expand( <sparseLU> )
35    
36            * NAMESPACE, man/all.equal-methods.Rd:
37            * R/Matrix.R (all.equal): methods for Matrices,
38            * R/sparseMatrix.R, R/sparseVector.R: sparseMatrices and -Vectors
39    
40    
41    2008-08-23  Douglas Bates <bates@stat.wisc.edu>
42    
43            * [r2243] R/CHMfactor.R, man/CHMfactor-class.Rd: Added expand method and
44              documentation for CHMfactor class
45            * [r2241] R/CHMfactor.R: Added trivial coercion method for CHMfactor ->
46              pMatrix
47    
48    2008-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/nsCMatrix.R (setAs(., dgTMatrix))): remove unused method
51    
52    2008-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/Ops.R (.Ops2dge.via.x, and many others): eliminate never-used
55            variable assignments {from "next version" codetools}.
56            * R/Csparse.R, R/Tsparse.R: ditto
57    
58    2008-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/sparseVector.R (sp2vec, coerce to sparseVector):
61            make sure no integer overflows happen, and use double precision
62            (n, index) where appropriate.
63    
64            * tests/Simple.R: test "large" sparse vectors.
65    
66    2008-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/AllClass.R (sparseVector): 'length' and 'i' are "numeric", not
69            just integer (allowing much longer length).
70    
71    2008-07-28  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/AllClass.R (diagonalMatrix): extend  "sparseMatrix" instead of
74            "denseMatrix".  This renders "scarceMatrix" dispensable and
75            invalidates part of MM's presentations on "space of Matrix
76            classes", but seems cleaner overall.
77    
78            * R/diagMatrix.R, etc: eliminate "scarceMatrix", replacing it by
79            "sparseMatrix" in method signatures;
80            further, instead of coercing to "sparseMatrix", coerce to
81            "TsparseMatrix" now.
82    
83    2008-07-26  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * src/dgCMatrix.c (dgCMatrix_qrsol): allow third argument 'order' in
86            .Call(.)
87            * R/sparseMatrix.R (lm.fit.sparse), src/dgCMatrix.h, src/init.c: ditto
88    
89    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
92            recursion in new test in
93            * tests/matprod.R: testing the above and another solve() case, below
94    
95            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
96            e.g. triangular 'x'.
97    
98            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
99            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
100            correctly with unit-triangular x
101    
102            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
103            instead of not checking diagU.
104    
105            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
106            experiments where diagonalMatrix would extend sparse*.
107    
108    
109    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
112            "x@p[ncol(x)]" instead of length(x@i).
113            * R/Auxiliaries.R (nnzero): ditto
114    
115            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
116            since that fails for over-allocated i.
117    
118            * tests/validObj.R: more testing of over-allocated (i,x) slots
119    
120    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
123            'sort_in_place' and set it to TRUE in call from
124            * src/Csparse.c (Csparse_validate): sort in place, making sure that
125            validObject() continues sort the columns if needed.
126    
127            * tests/validObj.R: now tests that more thoroughly, and
128            * man/CsparseMatrix-class.Rd: documents it.
129    
130    2008-07-22  Douglas Bates <bates@stat.wisc.edu>
131    
132            * [r2233] src/chm_common.c: sort columns more carefully in
133              as_cholmod_sparse
134            * [r2231] src/chm_common.c: check for sorted columns in
135              as_cholmod_sparse instead of assuming it
136            * [r2228] src/cs_utils.c: Use R_alloc for semi-permanent storage when
137              expanding diagonal
138    
139    
140    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
143            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
144            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
145            diagU2N().
146    
147            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
148            .spDiagonal() and new .trDiagonal().
149    
150            * R/dtCMatrix.R (solve): make use of .trDiagonal()
151    
152    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
155            stumbled upon by Michael H.
156    
157            * tests/validObj.R: testing the bug-fix
158    
159            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
160            versions.
161    
162            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
163            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
164    
165            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
166              AS_CHM_SP() which includes diagU2N.
167    
168            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
169            adapt to 3 arguments.
170    
171    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
172    
173            * [r2220] src/dtCMatrix.c: Correct number of columns for rhs in
174              dtCMatrix_sparse_solve
175            * [r2219] src/cs_utils.c: eye->nz should be -1 for compressed column
176              storage
177            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
178              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
179              new solve method
180            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
181              Csparse_diagU2N functionality into Matrix_as_cs
182    
183    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
186    
187    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
188    
189            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
190              argument with default TRUE
191            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
192              Csparse_diagU2N
193            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
194              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
195              parent array; new solve method for signature(a = "dtCMatrix", b =
196              "sparseMatrix")
197    
198    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/diagMatrix.R (.bdiag): also keep result triangular
201    
202    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
203    
204            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
205              messages
206    
207    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
210            symmetric- or nsparse-Matrix, also fixing the bug introduced with
211            the new version (.999375-10).
212    
213            * tests/Simple.R: regression test for the bugs.
214    
215    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * R/sparseVector.R (spV2M): fix for "isparseVector".
218            Further, fix <diag> -> <sparseVector> coercion
219            (repSpV): add rep(<sparseVector>, .) method
220    
221            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
222            use as.vector(.).
223    
224            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
225    
226            * R/AllClass.R: new (hidden) class union "scarceMatrix"
227            * R/AllClass.R: sparseVector: add prototype
228    
229            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
230            Kasper Kristensen
231    
232    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * tests/other-pkgs.R: add more interesting Matrix -> graph
235    
236    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
239            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
240    
241    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * DESCRIPTION: release 0.999375-10 to CRAN
244    
245            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
246            .bdiag().
247            * man/bdiag.Rd: update, including test.
248    
249    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * tests/Simple.R: add minimal bdiag() checks
252    
253            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
254              factor out the Tsparse - internal computation into new .bdiag()
255    
256    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * R/nsparseMatrix.R: specific fast all() and any() methods.
259    
260            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
261            when trying to produce too large result.
262    
263            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
264            very large matrices.
265    
266            * R/sparseMatrix.R (printSpMatrix2): new function, used by
267            show(<sparseMatrix>).
268    
269            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
270    
271    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * src/Mutils.c (m_encodeInd, m_encodeInd2):
274            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
275    
276            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
277            big matrices): -> 2nd argument 'di' instead of 'nr' !
278    
279    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/dtCMatrix.R: faster dgC* -> dtC* method
282            * tests/Simple.R: (hence removed "FIXME")
283    
284            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
285            which can be be turned off for possible speed gains.
286    
287    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
290    
291            * R/not.R: fix !<ldiMatrix>
292            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
293    
294            * R/diagMatrix.R (Ops): fix one-off thinko in
295            <diagonal> o <numeric> methods
296    
297            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
298    
299    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
302            * tests/Simple.R: testing the above
303    
304    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
307    
308    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
311            * NAMESPACE (unname): finally exported
312    
313    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/Auxiliaries.R (cholMat): possibly keep packed
316    
317            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
318            for R < 2.7.0.
319    
320            * R/Tsparse.R ([): for triangularMatrix, check if result may be
321            triangular.
322            * tests/indexing.R: regression test
323    
324    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
327            * R/Ops.R: more methods, for lMatrix/nMatrix
328    
329    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/expm.R: new file for all expm() methods; notably new ones for
332            diagonal*, triangular*, symmetric* and also simple "matrix".
333    
334    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
337    
338            * inst/test-tools.R (assert.EQ.mat): better message when not equal
339    
340            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
341    
342            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
343            [dl]denseMatrix {identical slots; but more logical method dispatch}
344    
345    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
348    
349            * R/diagMatrix.R (determinant): method
350    
351    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
354    
355            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
356    
357            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
358            its diagonal
359    
360    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
363    
364            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
365    
366            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
367    
368            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
369    
370    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
373    
374            * R/Ops.R (.do.Logic.lsparse): fix NA case
375    
376            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
377    
378            * R/Auxiliaries.R (nnzero): fix special cases, using
379            * R/Auxiliaries.R (indDiag): new utility
380            * R/Auxiliaries.R (indTri): new argument 'diag'
381    
382            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
383    
384    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
387    
388            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
389            ".tCMatrix" triangular matrix.
390    
391            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
392            'clx' can be class *or* class representation.
393            (nnzSparse): new.
394            (non0ind): new 'xtendSymm' argument; used in
395            * R/Ops.R:
396    
397            * R/pMatrix.R: more efficient determinant() method
398    
399    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
402            * [disactivated] NAMESPACE: export(det)
403    
404            * R/diagMatrix.R (mkDiag): new substitute for diag()
405    
406            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
407            (as0, as1): new utility.
408    
409            * R/Csparse.R (diag, band): need diagU2N()
410    
411            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
412    
413            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
414    
415            * R/Ops.R (Compare): fix <nsp> o <nsp> case
416    
417            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
418    
419    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * R/Auxiliaries.R (signPerm): new utility for
422            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
423    
424            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
425            since we have our own error handler (and can use tryCatch() from R).
426    
427    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
430    
431            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
432            when not positive definite.
433    
434            * R/Auxiliaries.R (asTri): new auxiliary
435            (non0.i): make *much* faster for Tsparse with many non-zero
436            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
437    
438            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
439            test-tools.R , see below
440    
441            * R/dMatrix.R: fix "Summary" method: + diagU2N()
442    
443            * NAMESPACE, R/Matrix.R: add mean() method
444    
445    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
448            cold-hot colors; try *changed* default useAbs = FALSE
449            * man/image-methods.Rd:  nice examples
450    
451    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * inst/test-tools.R (checkMatrix): new function for modularizing part
454            of tstMatrixClass() in tests/Class+Meth.R
455    
456            * R/dsCMatrix.R: coercion from "matrix"
457            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
458    
459            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
460            add test for as(matrix(,0,0), <class>)
461    
462    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
465            work as determinant(matrix(,0,0)).
466    
467            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
468            * man/sparseLU-class.Rd: ditto
469    
470            * R/dgCMatrix.R (determinant): method building on lu()
471            * R/sparseMatrix.R, Matrix.R, ...: ditto
472    
473            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
474    
475    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
478            pattern matrices.
479    
480    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * src/dense.c (dense_to_Csparse): all declarations *before*
483            R_CheckStack(); needed e.g. for ancient gcc 2.96.
484    
485    
486  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488          * DESCRIPTION (Version): 0.999375-9 --- need to release          * DESCRIPTION (Version): 0.999375-9 --- need to release
489          for R-devel (and R 2.7.0 alpha soon).          for R-devel (and R 2.7.0 alpha soon).
490    
491            * R/AllClass.R: drop "double" from "atomicVector" class union
492    
493            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
494            * R/dgeMatrix.R: ditto
495    
496          * R/sparseMatrix.R (summary): count NAs          * R/sparseMatrix.R (summary): count NAs
497    
498            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
499    
500  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in

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