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revision 1975, Mon Jul 9 20:52:50 2007 UTC revision 2123, Wed Mar 5 08:44:52 2008 UTC
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1    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
4    
5    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
8    
9            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
10            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
11    
12            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
13    
14            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
15    
16            * src/chm_common.c (AS_CHM_FINISH): add note about problem
17            for triangular (diag = "U").
18    
19    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
22            * R/bind.R:  .Call(dense_to_Csparse, *)
23    
24    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/Matrix.R (Matrix): no longer use coercions to specific classes
27                    (since we are discouraging them in user code).
28    
29            * tests/*.R: also replaces coercions to specific classes by
30            coercions to super classes.
31    
32            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
33    
34    
35    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
38    
39            * src/dense.c (dense_band): generalized from ddense_band
40    
41            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
42              now for "denseMatrix" (instead of just "ddense*"); much
43              simplified setMethod()s for these.
44    
45            * src/dense.c (dense_to_symmetric): generalized from ddense_*
46    
47    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
50            version of as(*, "symmetricMatric").
51    
52            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
53            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
54    
55    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/Matrix.R (subset.ij): utility, as first step to faster
58               M [ <ij-matrix> ] indexing.
59    
60            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
61    
62            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
63            for more efficient symmpart() and skewpart() methods.
64    
65            * src/Mutils.c (equal_string_vectors): utility
66    
67            * src/dense.c (ddense_to_symmetric): new function used in
68    
69            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
70    
71            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
72            order to match the generic (and evade .local(..)).
73    
74            * R/dsCMatrix.R: dgC -> dsC: use C code!
75    
76            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
77            as per TODO
78    
79            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
80    
81            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
82    
83    
84    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
87    
88            * R/Auxiliaries.R (non0.i): take out of non0ind
89    
90            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
91            make tril(), triu(), band() work for "matrix" and all "dense*"
92    
93            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
94            * tests/simple.R: test the fix above
95    
96            * R/sparseMatrix.R ([): simplification: no coerce to <general>
97                    before we use as(., <Tsparse>)[...] anyway
98    
99            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
100    
101            * R/triangularMatrix.R (isTriangular): methods for all subclasses
102            instead of "triangularMatrix" -- just to disambiguate
103    
104    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
107            * tests/indexing.R: example that fails above
108    
109    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
112            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
113                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
114    
115            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
116            * src/Tsparse.h, init.c: ditto
117            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
118                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
119            * R/sparseMatrix.R (isTriangular): hence simplified
120    
121    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/Ops.R (.Arith.Csparse): new utility factored out of former
124              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
125    
126    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
129    
130            * inst/test-tools.R (isOrthogonal): new function; also file restructured
131    
132    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
135            coercion to "nMatrix" and "pMatrix"
136    
137            * R/AllClass.R: "Schur" class;  "number" class union
138            * man/number-class.Rd:
139            * man/Schur-class.Rd:
140    
141            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
142            (.simpleSchur): Schur() method for diagonal matrices
143            (.triSchur):    Schur() method for triangular matrices
144            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
145    
146    
147    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
150    
151    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
154                    in order to ensure 'system = *' is not lost;
155                    formals()$system instead of cut&paste.
156            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
157    
158    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * DESCRIPTION (Date): make ready for release --> 0.999375-4
161    
162            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
163    
164    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
167                    and hence does as.vector(.).
168            * man/pMatrix-class.Rd: docs
169            * R/sparseMatrix.R: fix for printing "integer sparse"
170    
171            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
172    
173            * R/Matrix.R and others: use "exact" function argument list for
174                    both "["   : (x, i,j, ..., drop)
175                    and  "[<-" : (x, i,j, ..., value)
176    
177            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
178            * R/Tsparse.R (replTmat):    ditto
179            * R/diagMatrix.R (replDiag): ditto
180            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
181            * tests/indexing.R: testing the above
182    
183    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/sparseMatrix.R (cov2cor): method for sparse matrices
186    
187            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
188    
189            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
190    
191            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
192    
193    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * R/Matrix.R: "generic" cov2cor() method
196    
197            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
198                    speed up Q %*% D %*% t(Q)
199            * tests/dpoMatrix.R: test nearPD()
200    
201    2007-12-05  Doug Bates and Martin Maechler
202    
203            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
204            stats::xtabs() allowing to create sparse matrices.
205    
206    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
209    
210    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
213    
214    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/LU.R: solve() method for "denseLU"
217    
218    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * DESCRIPTION (Version): 0.999375-3 preparing for release
221    
222            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
223    
224            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
225    
226    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
229              thanks to Kasper Kristensen.
230            * tests/matprod.R: regression test for that.
231    
232    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
233    
234            * [r4778] R/AllGeneric.R: Check R version before defining generics for
235              primitives
236    
237    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * R/denseMatrix.R (rcond): method
240            * R/sparseQR.R (rcond): method, use x or t(x)
241    
242    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
245            matrices.
246            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
247    
248            * man/rcond.Rd: mention the more general definition, and add
249            example for non-square matrices.
250    
251            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
252    
253    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
256    
257    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
260            * tests/indexing.R: add new regression for the above cases.
261    
262    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * src/Mutils.h (__sun): clause for alloca.h on Solaris
265    
266    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
268            * DESCRIPTION (Date, Version): 0.999375-2
269    
270    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * R/HBMM.R (readMM): make work for pattern matrices as well
273    
274    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
275    
276            * [r4730] src/Mutils.h: declare alloca
277            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
278              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
279              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
280              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
281              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
282              methods; switch writeMM to use CHOLMOD code; repair readMM
283    
284    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
287            Oehlschlaegel's ... result type still to be discussed!
288    
289    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * man/image-methods.Rd: new, combining all image() methods
292    
293    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
296            to work via dgC...
297    
298            * R/Matrix.R (Matrix): special treatment for "table" (S3)
299    
300    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dgTMatrix.R (image): change defaults to
303                    aspect = "iso", colorkey = FALSE
304    
305    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
308            must copy its *expanded* x slot before LAPACK call.
309    
310            * tests/matprod.R: test the last days' changes.
311    
312    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
313    
314            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
315              as well as in sources
316            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
317              Lapack call
318    
319    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
322                    ("Matrix", "matrix") which is needed in some cases.
323            Ditto for solve().
324    
325            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
326            infinite recursion in dispatch for some cases.
327    
328    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
329    
330            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
331              so pointers match
332    
333    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * DESCRIPTION (Date): set ready for release -- 0.999375-1
336    
337    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
338    
339            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
340              src/chm_common.c, src/chm_common.h: Change API for
341              numeric_as_chm_dense and N_AS_CHM_DN
342    
343    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
346            * tests/matprod.R: regr.test for it
347    
348    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
351            * tests/group-methods.R: and regression-test it
352    
353    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
354    
355            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
356              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
357              triplet_to_sparse, documentation, use typedefs
358    
359    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * man/dpoMatrix-class.Rd: added 'corMatrix' example
362    
363            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
364            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
365            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
366    
367            * R/lsparseMatrix.R: bug fix in "all" method
368            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
369    
370            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
371            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
372                    + matrix |-> nMatrix coercion
373            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
374            * man/pMatrix-class.Rd: ditto
375    
376            * R/Matrix.R (Summary): method for non-dMatrix
377    
378            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
379            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
380                    test all Summary methods.
381    
382    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
385    
386    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
389    
390            * R/pMatrix.R (t?crossprod): methods for pMatrix
391    
392    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
393    
394            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
395    
396  2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>  2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
397    
398          * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums          * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
399            to fix a subtle bug (Kurt Hornik and Ingo Feinerer)            trying to fix a subtle bug - which has been somewhere else.
400    
401  2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>  2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
402    

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