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revision 1968, Sat Jul 7 22:49:12 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>
341    
342            * [r4730] src/Mutils.h: declare alloca
343            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
344              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
345              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
346              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
347              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
348              methods; switch writeMM to use CHOLMOD code; repair readMM
349    
350    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
353            Oehlschlaegel's ... result type still to be discussed!
354    
355    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * man/image-methods.Rd: new, combining all image() methods
358    
359    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
362            to work via dgC...
363    
364            * R/Matrix.R (Matrix): special treatment for "table" (S3)
365    
366    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/dgTMatrix.R (image): change defaults to
369                    aspect = "iso", colorkey = FALSE
370    
371    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
374            must copy its *expanded* x slot before LAPACK call.
375    
376            * tests/matprod.R: test the last days' changes.
377    
378    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
379    
380            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
381              as well as in sources
382            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
383              Lapack call
384    
385    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
388                    ("Matrix", "matrix") which is needed in some cases.
389            Ditto for solve().
390    
391            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
392            infinite recursion in dispatch for some cases.
393    
394    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
395    
396            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
397              so pointers match
398    
399    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * DESCRIPTION (Date): set ready for release -- 0.999375-1
402    
403    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
404    
405            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
406              src/chm_common.c, src/chm_common.h: Change API for
407              numeric_as_chm_dense and N_AS_CHM_DN
408    
409    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
412            * tests/matprod.R: regr.test for it
413    
414    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
417            * tests/group-methods.R: and regression-test it
418    
419    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
420    
421            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
422              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
423              triplet_to_sparse, documentation, use typedefs
424    
425    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * man/dpoMatrix-class.Rd: added 'corMatrix' example
428    
429            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
430            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
431            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
432    
433            * R/lsparseMatrix.R: bug fix in "all" method
434            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
435    
436            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
437            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
438                    + matrix |-> nMatrix coercion
439            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
440            * man/pMatrix-class.Rd: ditto
441    
442            * R/Matrix.R (Summary): method for non-dMatrix
443    
444            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
445            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
446                    test all Summary methods.
447    
448    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
451    
452    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
455    
456            * R/pMatrix.R (t?crossprod): methods for pMatrix
457    
458    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
459    
460            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
461    
462    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
463    
464            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
465              trying to fix a subtle bug - which has been somewhere else.
466    
467    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
468    
469            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
470              solve the bug
471    
472  2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474          * src/dgCMatrix.c (compressed_to_TMatrix):          * src/dgCMatrix.c (compressed_to_TMatrix):

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