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revision 2011, Fri Jul 20 12:56:10 2007 UTC revision 2165, Sat Mar 29 21:40:18 2008 UTC
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1    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.999375-9 --- need to release
4            for R-devel (and R 2.7.0 alpha soon).
5    
6            * R/AllClass.R: drop "double" from "atomicVector" class union
7    
8            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
9            * R/dgeMatrix.R: ditto
10    
11            * R/sparseMatrix.R (summary): count NAs
12    
13            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
14    
15    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
18            order to become compatible to new R 2.7.0 base::rcond().
19    
20    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
23    
24            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
25    
26            * inst/test-tools.R (isValid): new utility, used much in
27            * tests/simple.R:
28    
29            * man/BunchKaufman-methods.Rd: added too
30    
31    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/dsyMatrix.R: add BunchKaufman() methods.
34            * R/dspMatrix.R:
35    
36            * src/init.c: add dsyMatrix_trf
37    
38    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
39    
40            * DESCRIPTION (Version): release 0.999375-7
41            * src/CHMfactor.c (CHMfactor_update): fix
42    
43    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
46            internal_chm_factor().
47    
48            * R/AllGeneric.R: do *not* define a "chol" generic
49                    (but rather use the implicit one *without* making pivot
50                    part of the signature)
51            * R/*.R: drop the 'pivot' from chol's signature and make
52                    'pivot=FALSE' a default argument of method definitions.
53    
54            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
55            version of Matrix
56    
57    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
60    
61            * R/sparseMatrix.R (is.na): new simple method
62            * R/denseMatrix.R (is.na): ditto.
63    
64            * R/diagMatrix.R (.symDiagonal): newly exported utility.
65    
66            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
67    
68            * src/UFsparse_download.sh: -->
69            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
70    
71    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
74            functionality; barely tested in
75            * tests/factorizing.R
76    
77            * src/Csparse.c (diag_tC): new functionality to enable faster
78            determinant(<dsCMatrix>, .) in
79            * R/dsCMatrix.R
80    
81    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
82    
83            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
84              src/CHMfactor.c, src/CHMfactor.h,
85              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
86              Log-determinant of the parent matrix from a CHMfactor object as
87              chm_factor_ldetL2; documentation and support
88    
89    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
92    
93    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
96            warning.
97    
98    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
101    
102            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
103              <diagonal> o <sparse_triangular>
104              setAs(., "nMatrix") added.
105    
106            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
107    
108            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
109                    new argument 'checkDense = FALSE'.
110    
111    
112    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
115            back-permutation of the matrix exponential.
116    
117            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
118    
119            * DESCRIPTION (Date,Version): ready to release 0.999375-5
120    
121            * tests/simple.R: testing diagN2U
122    
123    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/Auxiliaries.R (diagN2U): interface to
126    
127            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
128    
129            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
130    
131    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * src/chm_common.c (chm_diagN2U): new utility.
134    
135            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
136            make use of chm_diagN2U() and hence now preserve triangularity and
137            unit-triangularity.
138    
139            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
140    
141    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
144    
145            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
146            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
147    
148            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
149    
150            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
151    
152            * src/chm_common.c (AS_CHM_FINISH): add note about problem
153            for triangular (diag = "U").
154    
155    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
158            * R/bind.R:  .Call(dense_to_Csparse, *)
159    
160    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/Matrix.R (Matrix): no longer use coercions to specific classes
163                    (since we are discouraging them in user code).
164    
165            * tests/*.R: also replaces coercions to specific classes by
166            coercions to super classes.
167    
168            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
169    
170    
171    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
174    
175            * src/dense.c (dense_band): generalized from ddense_band
176    
177            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
178              now for "denseMatrix" (instead of just "ddense*"); much
179              simplified setMethod()s for these.
180    
181            * src/dense.c (dense_to_symmetric): generalized from ddense_*
182    
183    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
186            version of as(*, "symmetricMatric").
187    
188            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
189            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
190    
191    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Matrix.R (subset.ij): utility, as first step to faster
194               M [ <ij-matrix> ] indexing.
195    
196            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
197    
198            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
199            for more efficient symmpart() and skewpart() methods.
200    
201            * src/Mutils.c (equal_string_vectors): utility
202    
203            * src/dense.c (ddense_to_symmetric): new function used in
204    
205            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
206    
207            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
208            order to match the generic (and evade .local(..)).
209    
210            * R/dsCMatrix.R: dgC -> dsC: use C code!
211    
212            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
213            as per TODO
214    
215            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
216    
217            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
218    
219    
220    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
223    
224            * R/Auxiliaries.R (non0.i): take out of non0ind
225    
226            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
227            make tril(), triu(), band() work for "matrix" and all "dense*"
228    
229            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
230            * tests/simple.R: test the fix above
231    
232            * R/sparseMatrix.R ([): simplification: no coerce to <general>
233                    before we use as(., <Tsparse>)[...] anyway
234    
235            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
236    
237            * R/triangularMatrix.R (isTriangular): methods for all subclasses
238            instead of "triangularMatrix" -- just to disambiguate
239    
240    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
243            * tests/indexing.R: example that fails above
244    
245    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
248            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
249                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
250    
251            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
252            * src/Tsparse.h, init.c: ditto
253            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
254                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
255            * R/sparseMatrix.R (isTriangular): hence simplified
256    
257    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/Ops.R (.Arith.Csparse): new utility factored out of former
260              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
261    
262    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
265    
266            * inst/test-tools.R (isOrthogonal): new function; also file restructured
267    
268    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
271            coercion to "nMatrix" and "pMatrix"
272    
273            * R/AllClass.R: "Schur" class;  "number" class union
274            * man/number-class.Rd:
275            * man/Schur-class.Rd:
276    
277            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
278            (.simpleSchur): Schur() method for diagonal matrices
279            (.triSchur):    Schur() method for triangular matrices
280            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
281    
282    
283    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
286    
287    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
290                    in order to ensure 'system = *' is not lost;
291                    formals()$system instead of cut&paste.
292            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
293    
294    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * DESCRIPTION (Date): make ready for release --> 0.999375-4
297    
298            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
299    
300    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
303                    and hence does as.vector(.).
304            * man/pMatrix-class.Rd: docs
305            * R/sparseMatrix.R: fix for printing "integer sparse"
306    
307            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
308    
309            * R/Matrix.R and others: use "exact" function argument list for
310                    both "["   : (x, i,j, ..., drop)
311                    and  "[<-" : (x, i,j, ..., value)
312    
313            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
314            * R/Tsparse.R (replTmat):    ditto
315            * R/diagMatrix.R (replDiag): ditto
316            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
317            * tests/indexing.R: testing the above
318    
319    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/sparseMatrix.R (cov2cor): method for sparse matrices
322    
323            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
324    
325            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
326    
327            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
328    
329    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/Matrix.R: "generic" cov2cor() method
332    
333            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
334                    speed up Q %*% D %*% t(Q)
335            * tests/dpoMatrix.R: test nearPD()
336    
337    2007-12-05  Doug Bates and Martin Maechler
338    
339            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
340            stats::xtabs() allowing to create sparse matrices.
341    
342    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
345    
346    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
349    
350    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/LU.R: solve() method for "denseLU"
353    
354    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * DESCRIPTION (Version): 0.999375-3 preparing for release
357    
358            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
359    
360            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
361    
362    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
365              thanks to Kasper Kristensen.
366            * tests/matprod.R: regression test for that.
367    
368    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
369    
370            * [r4778] R/AllGeneric.R: Check R version before defining generics for
371              primitives
372    
373    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/denseMatrix.R (rcond): method
376            * R/sparseQR.R (rcond): method, use x or t(x)
377    
378    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
381            matrices.
382            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
383    
384            * man/rcond.Rd: mention the more general definition, and add
385            example for non-square matrices.
386    
387            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
388    
389    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
392    
393    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
396            * tests/indexing.R: add new regression for the above cases.
397    
398    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * src/Mutils.h (__sun): clause for alloca.h on Solaris
401    
402    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * DESCRIPTION (Date, Version): 0.999375-2
405    
406    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/HBMM.R (readMM): make work for pattern matrices as well
409    
410    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
411    
412            * [r4730] src/Mutils.h: declare alloca
413            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
414              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
415              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
416              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
417              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
418              methods; switch writeMM to use CHOLMOD code; repair readMM
419    
420    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
423            Oehlschlaegel's ... result type still to be discussed!
424    
425    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * man/image-methods.Rd: new, combining all image() methods
428    
429    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
432            to work via dgC...
433    
434            * R/Matrix.R (Matrix): special treatment for "table" (S3)
435    
436    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/dgTMatrix.R (image): change defaults to
439                    aspect = "iso", colorkey = FALSE
440    
441    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
444            must copy its *expanded* x slot before LAPACK call.
445    
446            * tests/matprod.R: test the last days' changes.
447    
448    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
449    
450            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
451              as well as in sources
452            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
453              Lapack call
454    
455    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
458                    ("Matrix", "matrix") which is needed in some cases.
459            Ditto for solve().
460    
461            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
462            infinite recursion in dispatch for some cases.
463    
464    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
465    
466            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
467              so pointers match
468    
469    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * DESCRIPTION (Date): set ready for release -- 0.999375-1
472    
473    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
474    
475            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
476              src/chm_common.c, src/chm_common.h: Change API for
477              numeric_as_chm_dense and N_AS_CHM_DN
478    
479    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
482            * tests/matprod.R: regr.test for it
483    
484  2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
486          * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")          * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")

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