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revision 1966, Sat Jul 7 20:07:58 2007 UTC revision 2130, Fri Mar 14 19:27:16 2008 UTC
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1  2007-07-07 18:23  Douglas Bates <bates@stat.wisc.edu>  2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
4            warning.
5    
6    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
9    
10            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
11              <diagonal> o <sparse_triangular>
12              setAs(., "nMatrix") added.
13    
14            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
15    
16            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
17                    new argument 'checkDense = FALSE'.
18    
19    
20    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
23            back-permutation of the matrix exponential.
24    
25            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
26    
27            * DESCRIPTION (Date,Version): ready to release 0.999375-5
28    
29            * tests/simple.R: testing diagN2U
30    
31    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/Auxiliaries.R (diagN2U): interface to
34    
35            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
36    
37            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
38    
39    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * src/chm_common.c (chm_diagN2U): new utility.
42    
43            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
44            make use of chm_diagN2U() and hence now preserve triangularity and
45            unit-triangularity.
46    
47            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
48    
49    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
52    
53            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
54            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
55    
56            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
57    
58            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
59    
60            * src/chm_common.c (AS_CHM_FINISH): add note about problem
61            for triangular (diag = "U").
62    
63    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
66            * R/bind.R:  .Call(dense_to_Csparse, *)
67    
68    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/Matrix.R (Matrix): no longer use coercions to specific classes
71                    (since we are discouraging them in user code).
72    
73            * tests/*.R: also replaces coercions to specific classes by
74            coercions to super classes.
75    
76            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
77    
78    
79    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
82    
83            * src/dense.c (dense_band): generalized from ddense_band
84    
85            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
86              now for "denseMatrix" (instead of just "ddense*"); much
87              simplified setMethod()s for these.
88    
89            * src/dense.c (dense_to_symmetric): generalized from ddense_*
90    
91    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
94            version of as(*, "symmetricMatric").
95    
96            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
97            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
98    
99    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * R/Matrix.R (subset.ij): utility, as first step to faster
102               M [ <ij-matrix> ] indexing.
103    
104            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
105    
106            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
107            for more efficient symmpart() and skewpart() methods.
108    
109            * src/Mutils.c (equal_string_vectors): utility
110    
111            * src/dense.c (ddense_to_symmetric): new function used in
112    
113            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
114    
115            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
116            order to match the generic (and evade .local(..)).
117    
118            * R/dsCMatrix.R: dgC -> dsC: use C code!
119    
120            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
121            as per TODO
122    
123            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
124    
125            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
126    
127    
128    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
131    
132            * R/Auxiliaries.R (non0.i): take out of non0ind
133    
134            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
135            make tril(), triu(), band() work for "matrix" and all "dense*"
136    
137            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
138            * tests/simple.R: test the fix above
139    
140            * R/sparseMatrix.R ([): simplification: no coerce to <general>
141                    before we use as(., <Tsparse>)[...] anyway
142    
143            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
144    
145            * R/triangularMatrix.R (isTriangular): methods for all subclasses
146            instead of "triangularMatrix" -- just to disambiguate
147    
148    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
151            * tests/indexing.R: example that fails above
152    
153    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
156            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
157                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
158    
159            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
160            * src/Tsparse.h, init.c: ditto
161            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
162                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
163            * R/sparseMatrix.R (isTriangular): hence simplified
164    
165    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/Ops.R (.Arith.Csparse): new utility factored out of former
168              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
169    
170    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
173    
174            * inst/test-tools.R (isOrthogonal): new function; also file restructured
175    
176    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
179            coercion to "nMatrix" and "pMatrix"
180    
181            * R/AllClass.R: "Schur" class;  "number" class union
182            * man/number-class.Rd:
183            * man/Schur-class.Rd:
184    
185            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
186            (.simpleSchur): Schur() method for diagonal matrices
187            (.triSchur):    Schur() method for triangular matrices
188            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
189    
190    
191    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
194    
195    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
198                    in order to ensure 'system = *' is not lost;
199                    formals()$system instead of cut&paste.
200            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
201    
202    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * DESCRIPTION (Date): make ready for release --> 0.999375-4
205    
206            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
207    
208    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
211                    and hence does as.vector(.).
212            * man/pMatrix-class.Rd: docs
213            * R/sparseMatrix.R: fix for printing "integer sparse"
214    
215            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
216    
217            * R/Matrix.R and others: use "exact" function argument list for
218                    both "["   : (x, i,j, ..., drop)
219                    and  "[<-" : (x, i,j, ..., value)
220    
221            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
222            * R/Tsparse.R (replTmat):    ditto
223            * R/diagMatrix.R (replDiag): ditto
224            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
225            * tests/indexing.R: testing the above
226    
227    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/sparseMatrix.R (cov2cor): method for sparse matrices
230    
231            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
232    
233            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
234    
235            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
236    
237    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * R/Matrix.R: "generic" cov2cor() method
240    
241            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
242                    speed up Q %*% D %*% t(Q)
243            * tests/dpoMatrix.R: test nearPD()
244    
245    2007-12-05  Doug Bates and Martin Maechler
246    
247            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
248            stats::xtabs() allowing to create sparse matrices.
249    
250    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
253    
254    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
257    
258    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/LU.R: solve() method for "denseLU"
261    
262    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * DESCRIPTION (Version): 0.999375-3 preparing for release
265    
266            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
267    
268            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
269    
270    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
273              thanks to Kasper Kristensen.
274            * tests/matprod.R: regression test for that.
275    
276    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
277    
278            * [r4778] R/AllGeneric.R: Check R version before defining generics for
279              primitives
280    
281    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/denseMatrix.R (rcond): method
284            * R/sparseQR.R (rcond): method, use x or t(x)
285    
286    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
289            matrices.
290            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
291    
292            * man/rcond.Rd: mention the more general definition, and add
293            example for non-square matrices.
294    
295            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
296    
297    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
300    
301    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
304            * tests/indexing.R: add new regression for the above cases.
305    
306    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * src/Mutils.h (__sun): clause for alloca.h on Solaris
309    
310    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * DESCRIPTION (Date, Version): 0.999375-2
313    
314    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/HBMM.R (readMM): make work for pattern matrices as well
317    
318    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
319    
320            * [r4730] src/Mutils.h: declare alloca
321            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
322              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
323              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
324              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
325              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
326              methods; switch writeMM to use CHOLMOD code; repair readMM
327    
328    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
331            Oehlschlaegel's ... result type still to be discussed!
332    
333    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * man/image-methods.Rd: new, combining all image() methods
336    
337    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
340            to work via dgC...
341    
342            * R/Matrix.R (Matrix): special treatment for "table" (S3)
343    
344    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * R/dgTMatrix.R (image): change defaults to
347                    aspect = "iso", colorkey = FALSE
348    
349    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
352            must copy its *expanded* x slot before LAPACK call.
353    
354            * tests/matprod.R: test the last days' changes.
355    
356    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
357    
358            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
359              as well as in sources
360            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
361              Lapack call
362    
363    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
366                    ("Matrix", "matrix") which is needed in some cases.
367            Ditto for solve().
368    
369            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
370            infinite recursion in dispatch for some cases.
371    
372    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
373    
374            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
375              so pointers match
376    
377    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * DESCRIPTION (Date): set ready for release -- 0.999375-1
380    
381    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
382    
383            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
384              src/chm_common.c, src/chm_common.h: Change API for
385              numeric_as_chm_dense and N_AS_CHM_DN
386    
387    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
390            * tests/matprod.R: regr.test for it
391    
392    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
395            * tests/group-methods.R: and regression-test it
396    
397    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
398    
399            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
400              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
401              triplet_to_sparse, documentation, use typedefs
402    
403    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * man/dpoMatrix-class.Rd: added 'corMatrix' example
406    
407            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
408            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
409            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
410    
411            * R/lsparseMatrix.R: bug fix in "all" method
412            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
413    
414            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
415            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
416                    + matrix |-> nMatrix coercion
417            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
418            * man/pMatrix-class.Rd: ditto
419    
420            * R/Matrix.R (Summary): method for non-dMatrix
421    
422            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
423            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
424                    test all Summary methods.
425    
426    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
429    
430    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
433    
434            * R/pMatrix.R (t?crossprod): methods for pMatrix
435    
436    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
437    
438            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
439    
440    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
441    
442            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
443              trying to fix a subtle bug - which has been somewhere else.
444    
445    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
446    
447            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
448              solve the bug
449    
450    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * src/dgCMatrix.c (compressed_to_TMatrix):
453    
454    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
455    
456            * src/Csparse.c (Rsparse_validate): new, to have some validity
457            checking for RsparseMatrix
458            * src/dgCMatrix.c (xRMatrix_validate): ditto
459            * src/dtCMatrix.c (tRMatrix_validate): ditto
460    
461    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
462    
463          * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in          * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
464            lgRMatrix            lgRMatrix

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