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revision 2051, Tue Aug 14 22:23:53 2007 UTC revision 2137, Mon Mar 17 22:21:24 2008 UTC
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1    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
4            functionality; barely tested in
5            * tests/factorizing.R
6    
7            * src/Csparse.c (diag_tC): new functionality to enable faster
8            determinant(<dsCMatrix>, .) in
9            * R/dsCMatrix.R
10    
11    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
12    
13            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
14              src/CHMfactor.c, src/CHMfactor.h,
15              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
16              Log-determinant of the parent matrix from a CHMfactor object as
17              chm_factor_ldetL2; documentation and support
18    
19    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
22    
23    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
26            warning.
27    
28    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
31    
32            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
33              <diagonal> o <sparse_triangular>
34              setAs(., "nMatrix") added.
35    
36            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
37    
38            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
39                    new argument 'checkDense = FALSE'.
40    
41    
42    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
45            back-permutation of the matrix exponential.
46    
47            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
48    
49            * DESCRIPTION (Date,Version): ready to release 0.999375-5
50    
51            * tests/simple.R: testing diagN2U
52    
53    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/Auxiliaries.R (diagN2U): interface to
56    
57            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
58    
59            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
60    
61    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * src/chm_common.c (chm_diagN2U): new utility.
64    
65            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
66            make use of chm_diagN2U() and hence now preserve triangularity and
67            unit-triangularity.
68    
69            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
70    
71    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
74    
75            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
76            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
77    
78            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
79    
80            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
81    
82            * src/chm_common.c (AS_CHM_FINISH): add note about problem
83            for triangular (diag = "U").
84    
85    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
88            * R/bind.R:  .Call(dense_to_Csparse, *)
89    
90    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/Matrix.R (Matrix): no longer use coercions to specific classes
93                    (since we are discouraging them in user code).
94    
95            * tests/*.R: also replaces coercions to specific classes by
96            coercions to super classes.
97    
98            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
99    
100    
101    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
104    
105            * src/dense.c (dense_band): generalized from ddense_band
106    
107            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
108              now for "denseMatrix" (instead of just "ddense*"); much
109              simplified setMethod()s for these.
110    
111            * src/dense.c (dense_to_symmetric): generalized from ddense_*
112    
113    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
116            version of as(*, "symmetricMatric").
117    
118            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
119            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
120    
121    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/Matrix.R (subset.ij): utility, as first step to faster
124               M [ <ij-matrix> ] indexing.
125    
126            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
127    
128            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
129            for more efficient symmpart() and skewpart() methods.
130    
131            * src/Mutils.c (equal_string_vectors): utility
132    
133            * src/dense.c (ddense_to_symmetric): new function used in
134    
135            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
136    
137            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
138            order to match the generic (and evade .local(..)).
139    
140            * R/dsCMatrix.R: dgC -> dsC: use C code!
141    
142            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
143            as per TODO
144    
145            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
146    
147            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
148    
149    
150    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
153    
154            * R/Auxiliaries.R (non0.i): take out of non0ind
155    
156            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
157            make tril(), triu(), band() work for "matrix" and all "dense*"
158    
159            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
160            * tests/simple.R: test the fix above
161    
162            * R/sparseMatrix.R ([): simplification: no coerce to <general>
163                    before we use as(., <Tsparse>)[...] anyway
164    
165            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
166    
167            * R/triangularMatrix.R (isTriangular): methods for all subclasses
168            instead of "triangularMatrix" -- just to disambiguate
169    
170    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
173            * tests/indexing.R: example that fails above
174    
175    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
178            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
179                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
180    
181            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
182            * src/Tsparse.h, init.c: ditto
183            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
184                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
185            * R/sparseMatrix.R (isTriangular): hence simplified
186    
187    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/Ops.R (.Arith.Csparse): new utility factored out of former
190              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
191    
192    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
195    
196            * inst/test-tools.R (isOrthogonal): new function; also file restructured
197    
198    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
201            coercion to "nMatrix" and "pMatrix"
202    
203            * R/AllClass.R: "Schur" class;  "number" class union
204            * man/number-class.Rd:
205            * man/Schur-class.Rd:
206    
207            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
208            (.simpleSchur): Schur() method for diagonal matrices
209            (.triSchur):    Schur() method for triangular matrices
210            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
211    
212    
213    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
216    
217    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
220                    in order to ensure 'system = *' is not lost;
221                    formals()$system instead of cut&paste.
222            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
223    
224    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * DESCRIPTION (Date): make ready for release --> 0.999375-4
227    
228            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
229    
230    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
233                    and hence does as.vector(.).
234            * man/pMatrix-class.Rd: docs
235            * R/sparseMatrix.R: fix for printing "integer sparse"
236    
237            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
238    
239            * R/Matrix.R and others: use "exact" function argument list for
240                    both "["   : (x, i,j, ..., drop)
241                    and  "[<-" : (x, i,j, ..., value)
242    
243            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
244            * R/Tsparse.R (replTmat):    ditto
245            * R/diagMatrix.R (replDiag): ditto
246            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
247            * tests/indexing.R: testing the above
248    
249    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/sparseMatrix.R (cov2cor): method for sparse matrices
252    
253            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
254    
255            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
256    
257            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
258    
259    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/Matrix.R: "generic" cov2cor() method
262    
263            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
264                    speed up Q %*% D %*% t(Q)
265            * tests/dpoMatrix.R: test nearPD()
266    
267    2007-12-05  Doug Bates and Martin Maechler
268    
269            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
270            stats::xtabs() allowing to create sparse matrices.
271    
272    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
275    
276    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
279    
280    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/LU.R: solve() method for "denseLU"
283    
284    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * DESCRIPTION (Version): 0.999375-3 preparing for release
287    
288            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
289    
290            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
291    
292    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
295              thanks to Kasper Kristensen.
296            * tests/matprod.R: regression test for that.
297    
298    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
299    
300            * [r4778] R/AllGeneric.R: Check R version before defining generics for
301              primitives
302    
303    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/denseMatrix.R (rcond): method
306            * R/sparseQR.R (rcond): method, use x or t(x)
307    
308    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
311            matrices.
312            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
313    
314            * man/rcond.Rd: mention the more general definition, and add
315            example for non-square matrices.
316    
317            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
318    
319    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
322    
323    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
326            * tests/indexing.R: add new regression for the above cases.
327    
328    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * src/Mutils.h (__sun): clause for alloca.h on Solaris
331    
332    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * DESCRIPTION (Date, Version): 0.999375-2
335    
336    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/HBMM.R (readMM): make work for pattern matrices as well
339    
340  2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>  2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
341    
342          * [r4730] src/Mutils.h: declare alloca          * [r4730] src/Mutils.h: declare alloca

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