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revision 2050, Tue Aug 14 22:23:33 2007 UTC revision 2158, Fri Mar 28 17:07:54 2008 UTC
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1    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
4            order to become compatible to new R 2.7.0 base::rcond().
5    
6    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
9    
10            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
11    
12            * inst/test-tools.R (isValid): new utility, used much in
13            * tests/simple.R:
14    
15            * man/BunchKaufman-methods.Rd: added too
16    
17    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/dsyMatrix.R: add BunchKaufman() methods.
20            * R/dspMatrix.R:
21    
22            * src/init.c: add dsyMatrix_trf
23    
24    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
25    
26            * DESCRIPTION (Version): release 0.999375-7
27            * src/CHMfactor.c (CHMfactor_update): fix
28    
29    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
32            internal_chm_factor().
33    
34            * R/AllGeneric.R: do *not* define a "chol" generic
35                    (but rather use the implicit one *without* making pivot
36                    part of the signature)
37            * R/*.R: drop the 'pivot' from chol's signature and make
38                    'pivot=FALSE' a default argument of method definitions.
39    
40            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
41            version of Matrix
42    
43    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
46    
47            * R/sparseMatrix.R (is.na): new simple method
48            * R/denseMatrix.R (is.na): ditto.
49    
50            * R/diagMatrix.R (.symDiagonal): newly exported utility.
51    
52            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
53    
54            * src/UFsparse_download.sh: -->
55            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
56    
57    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
60            functionality; barely tested in
61            * tests/factorizing.R
62    
63            * src/Csparse.c (diag_tC): new functionality to enable faster
64            determinant(<dsCMatrix>, .) in
65            * R/dsCMatrix.R
66    
67    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
68    
69            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
70              src/CHMfactor.c, src/CHMfactor.h,
71              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
72              Log-determinant of the parent matrix from a CHMfactor object as
73              chm_factor_ldetL2; documentation and support
74    
75    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
78    
79    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
82            warning.
83    
84    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
87    
88            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
89              <diagonal> o <sparse_triangular>
90              setAs(., "nMatrix") added.
91    
92            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
93    
94            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
95                    new argument 'checkDense = FALSE'.
96    
97    
98    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
101            back-permutation of the matrix exponential.
102    
103            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
104    
105            * DESCRIPTION (Date,Version): ready to release 0.999375-5
106    
107            * tests/simple.R: testing diagN2U
108    
109    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/Auxiliaries.R (diagN2U): interface to
112    
113            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
114    
115            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
116    
117    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * src/chm_common.c (chm_diagN2U): new utility.
120    
121            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
122            make use of chm_diagN2U() and hence now preserve triangularity and
123            unit-triangularity.
124    
125            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
126    
127    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
130    
131            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
132            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
133    
134            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
135    
136            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
137    
138            * src/chm_common.c (AS_CHM_FINISH): add note about problem
139            for triangular (diag = "U").
140    
141    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
144            * R/bind.R:  .Call(dense_to_Csparse, *)
145    
146    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Matrix.R (Matrix): no longer use coercions to specific classes
149                    (since we are discouraging them in user code).
150    
151            * tests/*.R: also replaces coercions to specific classes by
152            coercions to super classes.
153    
154            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
155    
156    
157    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
160    
161            * src/dense.c (dense_band): generalized from ddense_band
162    
163            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
164              now for "denseMatrix" (instead of just "ddense*"); much
165              simplified setMethod()s for these.
166    
167            * src/dense.c (dense_to_symmetric): generalized from ddense_*
168    
169    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
172            version of as(*, "symmetricMatric").
173    
174            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
175            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
176    
177    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/Matrix.R (subset.ij): utility, as first step to faster
180               M [ <ij-matrix> ] indexing.
181    
182            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
183    
184            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
185            for more efficient symmpart() and skewpart() methods.
186    
187            * src/Mutils.c (equal_string_vectors): utility
188    
189            * src/dense.c (ddense_to_symmetric): new function used in
190    
191            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
192    
193            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
194            order to match the generic (and evade .local(..)).
195    
196            * R/dsCMatrix.R: dgC -> dsC: use C code!
197    
198            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
199            as per TODO
200    
201            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
202    
203            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
204    
205    
206    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
209    
210            * R/Auxiliaries.R (non0.i): take out of non0ind
211    
212            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
213            make tril(), triu(), band() work for "matrix" and all "dense*"
214    
215            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
216            * tests/simple.R: test the fix above
217    
218            * R/sparseMatrix.R ([): simplification: no coerce to <general>
219                    before we use as(., <Tsparse>)[...] anyway
220    
221            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
222    
223            * R/triangularMatrix.R (isTriangular): methods for all subclasses
224            instead of "triangularMatrix" -- just to disambiguate
225    
226    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
229            * tests/indexing.R: example that fails above
230    
231    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
234            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
235                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
236    
237            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
238            * src/Tsparse.h, init.c: ditto
239            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
240                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
241            * R/sparseMatrix.R (isTriangular): hence simplified
242    
243    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/Ops.R (.Arith.Csparse): new utility factored out of former
246              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
247    
248    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
251    
252            * inst/test-tools.R (isOrthogonal): new function; also file restructured
253    
254    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
257            coercion to "nMatrix" and "pMatrix"
258    
259            * R/AllClass.R: "Schur" class;  "number" class union
260            * man/number-class.Rd:
261            * man/Schur-class.Rd:
262    
263            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
264            (.simpleSchur): Schur() method for diagonal matrices
265            (.triSchur):    Schur() method for triangular matrices
266            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
267    
268    
269    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
272    
273    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
276                    in order to ensure 'system = *' is not lost;
277                    formals()$system instead of cut&paste.
278            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
279    
280    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * DESCRIPTION (Date): make ready for release --> 0.999375-4
283    
284            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
285    
286    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
289                    and hence does as.vector(.).
290            * man/pMatrix-class.Rd: docs
291            * R/sparseMatrix.R: fix for printing "integer sparse"
292    
293            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
294    
295            * R/Matrix.R and others: use "exact" function argument list for
296                    both "["   : (x, i,j, ..., drop)
297                    and  "[<-" : (x, i,j, ..., value)
298    
299            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
300            * R/Tsparse.R (replTmat):    ditto
301            * R/diagMatrix.R (replDiag): ditto
302            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
303            * tests/indexing.R: testing the above
304    
305    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/sparseMatrix.R (cov2cor): method for sparse matrices
308    
309            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
310    
311            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
312    
313            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
314    
315    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/Matrix.R: "generic" cov2cor() method
318    
319            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
320                    speed up Q %*% D %*% t(Q)
321            * tests/dpoMatrix.R: test nearPD()
322    
323    2007-12-05  Doug Bates and Martin Maechler
324    
325            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
326            stats::xtabs() allowing to create sparse matrices.
327    
328    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
331    
332    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
335    
336    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/LU.R: solve() method for "denseLU"
339    
340    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * DESCRIPTION (Version): 0.999375-3 preparing for release
343    
344            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
345    
346            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
347    
348    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
351              thanks to Kasper Kristensen.
352            * tests/matprod.R: regression test for that.
353    
354    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
355    
356            * [r4778] R/AllGeneric.R: Check R version before defining generics for
357              primitives
358    
359    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/denseMatrix.R (rcond): method
362            * R/sparseQR.R (rcond): method, use x or t(x)
363    
364    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
367            matrices.
368            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
369    
370            * man/rcond.Rd: mention the more general definition, and add
371            example for non-square matrices.
372    
373            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
374    
375    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
378    
379    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
382            * tests/indexing.R: add new regression for the above cases.
383    
384    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * src/Mutils.h (__sun): clause for alloca.h on Solaris
387    
388    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * DESCRIPTION (Date, Version): 0.999375-2
391    
392    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * R/HBMM.R (readMM): make work for pattern matrices as well
395    
396  2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>  2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
397    
398          * [r4730] src/Mutils.h: declare alloca          * [r4730] src/Mutils.h: declare alloca
# Line 8  Line 403 
403            src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its            src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
404            methods; switch writeMM to use CHOLMOD code; repair readMM            methods; switch writeMM to use CHOLMOD code; repair readMM
405    
   
406  2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408          * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens          * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens

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