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revision 1852, Mon May 21 16:42:35 2007 UTC revision 2188, Mon Apr 28 13:42:12 2008 UTC
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1    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
4            for R < 2.7.0.
5    
6            * R/Tsparse.R ([): for triangularMatrix, check if result may be
7            triangular.
8            * tests/indexing.R: regression test
9    
10    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
13            * R/Ops.R: more methods, for lMatrix/nMatrix
14    
15    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/expm.R: new file for all expm() methods; notably new ones for
18            diagonal*, triangular*, symmetric* and also simple "matrix".
19    
20    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
23    
24            * inst/test-tools.R (assert.EQ.mat): better message when not equal
25    
26            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
27    
28            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
29            [dl]denseMatrix {identical slots; but more logical method dispatch}
30    
31    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
34    
35            * R/diagMatrix.R (determinant): method
36    
37    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
40    
41            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
42    
43            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
44            its diagonal
45    
46    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
49    
50            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
51    
52            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
53    
54            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
55    
56    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
59    
60            * R/Ops.R (.do.Logic.lsparse): fix NA case
61    
62            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
63    
64            * R/Auxiliaries.R (nnzero): fix special cases, using
65            * R/Auxiliaries.R (indDiag): new utility
66            * R/Auxiliaries.R (indTri): new argument 'diag'
67    
68            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
69    
70    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
73    
74            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
75            ".tCMatrix" triangular matrix.
76    
77            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
78            'clx' can be class *or* class representation.
79            (nnzSparse): new.
80            (non0ind): new 'xtendSymm' argument; used in
81            * R/Ops.R:
82    
83            * R/pMatrix.R: more efficient determinant() method
84    
85    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
88            * [disactivated] NAMESPACE: export(det)
89    
90            * R/diagMatrix.R (mkDiag): new substitute for diag()
91    
92            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
93            (as0, as1): new utility.
94    
95            * R/Csparse.R (diag, band): need diagU2N()
96    
97            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
98    
99            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
100    
101            * R/Ops.R (Compare): fix <nsp> o <nsp> case
102    
103            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
104    
105    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/Auxiliaries.R (signPerm): new utility for
108            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
109    
110            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
111            since we have our own error handler (and can use tryCatch() from R).
112    
113    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
116    
117            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
118            when not positive definite.
119    
120            * R/Auxiliaries.R (asTri): new auxiliary
121            (non0.i): make *much* faster for Tsparse with many non-zero
122            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
123    
124            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
125            test-tools.R , see below
126    
127            * R/dMatrix.R: fix "Summary" method: + diagU2N()
128    
129            * NAMESPACE, R/Matrix.R: add mean() method
130    
131    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
134            cold-hot colors; try *changed* default useAbs = FALSE
135            * man/image-methods.Rd:  nice examples
136    
137    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * inst/test-tools.R (checkMatrix): new function for modularizing part
140            of tstMatrixClass() in tests/Class+Meth.R
141    
142            * R/dsCMatrix.R: coercion from "matrix"
143            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
144    
145            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
146            add test for as(matrix(,0,0), <class>)
147    
148    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
151            work as determinant(matrix(,0,0)).
152    
153            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
154            * man/sparseLU-class.Rd: ditto
155    
156            * R/dgCMatrix.R (determinant): method building on lu()
157            * R/sparseMatrix.R, Matrix.R, ...: ditto
158    
159            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
160    
161    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
164            pattern matrices.
165    
166    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * src/dense.c (dense_to_Csparse): all declarations *before*
169            R_CheckStack(); needed e.g. for ancient gcc 2.96.
170    
171    
172    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * DESCRIPTION (Version): 0.999375-9 --- need to release
175            for R-devel (and R 2.7.0 alpha soon).
176    
177            * R/AllClass.R: drop "double" from "atomicVector" class union
178    
179            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
180            * R/dgeMatrix.R: ditto
181    
182            * R/sparseMatrix.R (summary): count NAs
183    
184            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
185    
186    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
189            order to become compatible to new R 2.7.0 base::rcond().
190    
191    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
194    
195            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
196    
197            * inst/test-tools.R (isValid): new utility, used much in
198            * tests/simple.R:
199    
200            * man/BunchKaufman-methods.Rd: added too
201    
202    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/dsyMatrix.R: add BunchKaufman() methods.
205            * R/dspMatrix.R:
206    
207            * src/init.c: add dsyMatrix_trf
208    
209    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
210    
211            * DESCRIPTION (Version): release 0.999375-7
212            * src/CHMfactor.c (CHMfactor_update): fix
213    
214    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
217            internal_chm_factor().
218    
219            * R/AllGeneric.R: do *not* define a "chol" generic
220                    (but rather use the implicit one *without* making pivot
221                    part of the signature)
222            * R/*.R: drop the 'pivot' from chol's signature and make
223                    'pivot=FALSE' a default argument of method definitions.
224    
225            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
226            version of Matrix
227    
228    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
231    
232            * R/sparseMatrix.R (is.na): new simple method
233            * R/denseMatrix.R (is.na): ditto.
234    
235            * R/diagMatrix.R (.symDiagonal): newly exported utility.
236    
237            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
238    
239            * src/UFsparse_download.sh: -->
240            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
241    
242    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
245            functionality; barely tested in
246            * tests/factorizing.R
247    
248            * src/Csparse.c (diag_tC): new functionality to enable faster
249            determinant(<dsCMatrix>, .) in
250            * R/dsCMatrix.R
251    
252    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
253    
254            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
255              src/CHMfactor.c, src/CHMfactor.h,
256              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
257              Log-determinant of the parent matrix from a CHMfactor object as
258              chm_factor_ldetL2; documentation and support
259    
260    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
263    
264    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
267            warning.
268    
269    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
272    
273            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
274              <diagonal> o <sparse_triangular>
275              setAs(., "nMatrix") added.
276    
277            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
278    
279            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
280                    new argument 'checkDense = FALSE'.
281    
282    
283    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
286            back-permutation of the matrix exponential.
287    
288            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
289    
290            * DESCRIPTION (Date,Version): ready to release 0.999375-5
291    
292            * tests/simple.R: testing diagN2U
293    
294    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/Auxiliaries.R (diagN2U): interface to
297    
298            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
299    
300            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
301    
302    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * src/chm_common.c (chm_diagN2U): new utility.
305    
306            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
307            make use of chm_diagN2U() and hence now preserve triangularity and
308            unit-triangularity.
309    
310            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
311    
312    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
315    
316            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
317            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
318    
319            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
320    
321            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
322    
323            * src/chm_common.c (AS_CHM_FINISH): add note about problem
324            for triangular (diag = "U").
325    
326    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
329            * R/bind.R:  .Call(dense_to_Csparse, *)
330    
331    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * R/Matrix.R (Matrix): no longer use coercions to specific classes
334                    (since we are discouraging them in user code).
335    
336            * tests/*.R: also replaces coercions to specific classes by
337            coercions to super classes.
338    
339            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
340    
341    
342    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
345    
346            * src/dense.c (dense_band): generalized from ddense_band
347    
348            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
349              now for "denseMatrix" (instead of just "ddense*"); much
350              simplified setMethod()s for these.
351    
352            * src/dense.c (dense_to_symmetric): generalized from ddense_*
353    
354    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
357            version of as(*, "symmetricMatric").
358    
359            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
360            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
361    
362    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * R/Matrix.R (subset.ij): utility, as first step to faster
365               M [ <ij-matrix> ] indexing.
366    
367            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
368    
369            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
370            for more efficient symmpart() and skewpart() methods.
371    
372            * src/Mutils.c (equal_string_vectors): utility
373    
374            * src/dense.c (ddense_to_symmetric): new function used in
375    
376            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
377    
378            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
379            order to match the generic (and evade .local(..)).
380    
381            * R/dsCMatrix.R: dgC -> dsC: use C code!
382    
383            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
384            as per TODO
385    
386            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
387    
388            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
389    
390    
391    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
394    
395            * R/Auxiliaries.R (non0.i): take out of non0ind
396    
397            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
398            make tril(), triu(), band() work for "matrix" and all "dense*"
399    
400            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
401            * tests/simple.R: test the fix above
402    
403            * R/sparseMatrix.R ([): simplification: no coerce to <general>
404                    before we use as(., <Tsparse>)[...] anyway
405    
406            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
407    
408            * R/triangularMatrix.R (isTriangular): methods for all subclasses
409            instead of "triangularMatrix" -- just to disambiguate
410    
411    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
414            * tests/indexing.R: example that fails above
415    
416    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
419            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
420                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
421    
422            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
423            * src/Tsparse.h, init.c: ditto
424            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
425                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
426            * R/sparseMatrix.R (isTriangular): hence simplified
427    
428    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430            * R/Ops.R (.Arith.Csparse): new utility factored out of former
431              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
432    
433    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
436    
437            * inst/test-tools.R (isOrthogonal): new function; also file restructured
438    
439    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
442            coercion to "nMatrix" and "pMatrix"
443    
444            * R/AllClass.R: "Schur" class;  "number" class union
445            * man/number-class.Rd:
446            * man/Schur-class.Rd:
447    
448            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
449            (.simpleSchur): Schur() method for diagonal matrices
450            (.triSchur):    Schur() method for triangular matrices
451            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
452    
453    
454    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
455    
456            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
457    
458    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
461                    in order to ensure 'system = *' is not lost;
462                    formals()$system instead of cut&paste.
463            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
464    
465    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * DESCRIPTION (Date): make ready for release --> 0.999375-4
468    
469            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
470    
471    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
472    
473            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
474                    and hence does as.vector(.).
475            * man/pMatrix-class.Rd: docs
476            * R/sparseMatrix.R: fix for printing "integer sparse"
477    
478            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
479    
480            * R/Matrix.R and others: use "exact" function argument list for
481                    both "["   : (x, i,j, ..., drop)
482                    and  "[<-" : (x, i,j, ..., value)
483    
484            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
485            * R/Tsparse.R (replTmat):    ditto
486            * R/diagMatrix.R (replDiag): ditto
487            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
488            * tests/indexing.R: testing the above
489    
490    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/sparseMatrix.R (cov2cor): method for sparse matrices
493    
494            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
495    
496            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
497    
498            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
499    
500    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * R/Matrix.R: "generic" cov2cor() method
503    
504            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
505                    speed up Q %*% D %*% t(Q)
506            * tests/dpoMatrix.R: test nearPD()
507    
508    2007-12-05  Doug Bates and Martin Maechler
509    
510            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
511            stats::xtabs() allowing to create sparse matrices.
512    
513    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
516    
517    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
520    
521    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
522    
523            * R/LU.R: solve() method for "denseLU"
524    
525    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * DESCRIPTION (Version): 0.999375-3 preparing for release
528    
529            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
530    
531            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
532    
533    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
536              thanks to Kasper Kristensen.
537            * tests/matprod.R: regression test for that.
538    
539    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
540    
541            * [r4778] R/AllGeneric.R: Check R version before defining generics for
542              primitives
543    
544    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
545    
546            * R/denseMatrix.R (rcond): method
547            * R/sparseQR.R (rcond): method, use x or t(x)
548    
549    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
552            matrices.
553            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
554    
555            * man/rcond.Rd: mention the more general definition, and add
556            example for non-square matrices.
557    
558            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
559    
560    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
563    
564    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
565    
566            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
567            * tests/indexing.R: add new regression for the above cases.
568    
569    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * src/Mutils.h (__sun): clause for alloca.h on Solaris
572    
573    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
574    
575            * DESCRIPTION (Date, Version): 0.999375-2
576    
577    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * R/HBMM.R (readMM): make work for pattern matrices as well
580    
581    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
582    
583            * [r4730] src/Mutils.h: declare alloca
584            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
585              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
586              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
587              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
588              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
589              methods; switch writeMM to use CHOLMOD code; repair readMM
590    
591    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
594            Oehlschlaegel's ... result type still to be discussed!
595    
596    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * man/image-methods.Rd: new, combining all image() methods
599    
600    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
601    
602            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
603            to work via dgC...
604    
605            * R/Matrix.R (Matrix): special treatment for "table" (S3)
606    
607    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * R/dgTMatrix.R (image): change defaults to
610                    aspect = "iso", colorkey = FALSE
611    
612    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
615            must copy its *expanded* x slot before LAPACK call.
616    
617            * tests/matprod.R: test the last days' changes.
618    
619    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
620    
621            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
622              as well as in sources
623            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
624              Lapack call
625    
626    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
629                    ("Matrix", "matrix") which is needed in some cases.
630            Ditto for solve().
631    
632            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
633            infinite recursion in dispatch for some cases.
634    
635    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
636    
637            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
638              so pointers match
639    
640    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * DESCRIPTION (Date): set ready for release -- 0.999375-1
643    
644    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
645    
646            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
647              src/chm_common.c, src/chm_common.h: Change API for
648              numeric_as_chm_dense and N_AS_CHM_DN
649    
650    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
653            * tests/matprod.R: regr.test for it
654    
655    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
658            * tests/group-methods.R: and regression-test it
659    
660    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
661    
662            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
663              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
664              triplet_to_sparse, documentation, use typedefs
665    
666    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * man/dpoMatrix-class.Rd: added 'corMatrix' example
669    
670            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
671            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
672            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
673    
674            * R/lsparseMatrix.R: bug fix in "all" method
675            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
676    
677            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
678            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
679                    + matrix |-> nMatrix coercion
680            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
681            * man/pMatrix-class.Rd: ditto
682    
683            * R/Matrix.R (Summary): method for non-dMatrix
684    
685            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
686            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
687                    test all Summary methods.
688    
689    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
690    
691            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
692    
693    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
696    
697            * R/pMatrix.R (t?crossprod): methods for pMatrix
698    
699    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
700    
701            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
702    
703    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
704    
705            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
706              trying to fix a subtle bug - which has been somewhere else.
707    
708    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
709    
710            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
711              solve the bug
712    
713    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * src/dgCMatrix.c (compressed_to_TMatrix):
716    
717    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
718    
719            * src/Csparse.c (Rsparse_validate): new, to have some validity
720            checking for RsparseMatrix
721            * src/dgCMatrix.c (xRMatrix_validate): ditto
722            * src/dtCMatrix.c (tRMatrix_validate): ditto
723    
724    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
725    
726            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
727              lgRMatrix
728            * [r4568] DESCRIPTION: Prepare for bug-fix release
729            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
730              for declaration of cholmod_symmetry
731    
732    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
735            release.
736    
737    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
738    
739            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
740              functions - no longer used
741            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
742              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
743              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
744              Alloca
745    
746    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
747    
748            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
749              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
750              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
751              src/t_gCMatrix_colSums.c: more R_CheckStack()s
752    
753    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
754    
755            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
756              the required amount of memory then call M_numeric_as_chm_dense.
757            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
758              (like Calloc but calling alloca)
759    
760    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
761    
762            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
763            and extended with more sophisticated 'col.names' option.
764            * NAMESPACE: export  printSparseMatrix()
765            * man/printSpMatrix.Rd: document, incl. examples
766    
767    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
768    
769            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
770              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
771              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
772    
773    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * DESCRIPTION (Version): 0.99875-4
776    
777            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
778            some dimnames perservation.
779    
780            * R/dsTMatrix.R (t-method): keep dimnames
781            * R/dtTMatrix.R:  ditto
782    
783            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
784            and ncol(.) < 10
785    
786            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
787            from Mutils.h
788    
789            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
790            e.g. in as(<ngCMatrix>, "matrix")
791    
792    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
793    
794            * [r4529] .: Create a branch for the API changes from the 0.99875
795              series to the 0.999375 series
796            * [r4530] DESCRIPTION, inst/include/Matrix.h,
797              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
798              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
799              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
800              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
801              as_cholmod_x functions
802    
803    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
804    
805            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
806              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
807              to Comparisons
808    
809    >>>>>>> .merge-right.r4561
810    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
811    
812            * DESCRIPTION (Version): 0.99875-3 ready to be released.
813    
814            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
815    
816            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
817            that should also work in a future version of R.
818    
819    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
820    
821            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
822    
823            * R/sparseVector.R: more *sparseVector coercions, notably for
824            non - double ones.
825    
826    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
827    
828            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
829              notably the new ones building on the new .Call(.)s:
830    
831            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
832            all 4 of [dlin]gCMatrix_colSums().
833    
834    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
835    
836            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
837            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
838              result
839    
840    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
841    
842            * R/kronecker.R: fix typo (could lead to inf.recursion)
843            * test/simple.R: testing that
844    
845            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
846            method as well (which can have arguments, show() can't).
847    
848    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
849    
850            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
851              added dgCMatrix_colSums for [col,row][Sums,Means]
852    
853    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
854    
855            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
856              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
857              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
858            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
859              class
860            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
861              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
862              row names to store the levels - duh!  Added an example.
863    
864    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
865    
866            * src/Csparse.c (Csparse_validate): check for *repeated* entries
867            thanks to example from Christian Buchta; with a test here:
868            * tests/simple.R:
869    
870    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
871    
872            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
873            of colSums(*, sparseResult = TRUE)
874    
875    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
876    
877            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
878            'na.rm = FALSE' as "everywhere" else in R.
879    
880    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
881    
882            * [r4421] src/CSparse_install.sh: Modify for new organization of
883              CSparse package
884            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
885              SuiteSparse
886            * [r4426] src/Makefile: add ./UFconfig to the include path for
887              compilation
888            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
889            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
890              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
891    
892    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
893    
894            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
895            * R/sparseMatrix.R (prSpMatrix): now gives a message about
896            suppressed column names.
897    
898    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
899    
900            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
901              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
902              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
903              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
904              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
905              Remove warnings after change to const char* CHAR
906    
907    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
908    
909            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
910              type of M_cholmod_ssmult
911    
912    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
913    
914            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
915              src/init.c: Yet another cholmod export - cholmod_ssmult
916    
917    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
918    
919            * NAMESPACE: exported drop0(), since
920            * man/drop0.Rd: I have seen several cases, I really wanted to use
921            it, so our users may want too.
922    
923    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
924    
925            * man/colSums.Rd: separately document colSums() etc, since these
926            have the extra argument 'sparseResult'.
927    
928  2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
929    
930          * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;          * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;

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