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revision 2005, Wed Jul 18 14:46:20 2007 UTC revision 2125, Fri Mar 7 07:58:26 2008 UTC
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1    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/simple.R: testing diagN2U
4    
5    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Auxiliaries.R (diagN2U): interface to
8    
9            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
10    
11            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
12    
13    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * src/chm_common.c (chm_diagN2U): new utility.
16    
17            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
18            make use of chm_diagN2U() and hence now preserve triangularity and
19            unit-triangularity.
20    
21            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
22    
23    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
26    
27            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
28            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
29    
30            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
31    
32            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
33    
34            * src/chm_common.c (AS_CHM_FINISH): add note about problem
35            for triangular (diag = "U").
36    
37    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
40            * R/bind.R:  .Call(dense_to_Csparse, *)
41    
42    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/Matrix.R (Matrix): no longer use coercions to specific classes
45                    (since we are discouraging them in user code).
46    
47            * tests/*.R: also replaces coercions to specific classes by
48            coercions to super classes.
49    
50            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
51    
52    
53    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
56    
57            * src/dense.c (dense_band): generalized from ddense_band
58    
59            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
60              now for "denseMatrix" (instead of just "ddense*"); much
61              simplified setMethod()s for these.
62    
63            * src/dense.c (dense_to_symmetric): generalized from ddense_*
64    
65    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
68            version of as(*, "symmetricMatric").
69    
70            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
71            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
72    
73    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/Matrix.R (subset.ij): utility, as first step to faster
76               M [ <ij-matrix> ] indexing.
77    
78            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
79    
80            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
81            for more efficient symmpart() and skewpart() methods.
82    
83            * src/Mutils.c (equal_string_vectors): utility
84    
85            * src/dense.c (ddense_to_symmetric): new function used in
86    
87            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
88    
89            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
90            order to match the generic (and evade .local(..)).
91    
92            * R/dsCMatrix.R: dgC -> dsC: use C code!
93    
94            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
95            as per TODO
96    
97            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
98    
99            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
100    
101    
102    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
105    
106            * R/Auxiliaries.R (non0.i): take out of non0ind
107    
108            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
109            make tril(), triu(), band() work for "matrix" and all "dense*"
110    
111            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
112            * tests/simple.R: test the fix above
113    
114            * R/sparseMatrix.R ([): simplification: no coerce to <general>
115                    before we use as(., <Tsparse>)[...] anyway
116    
117            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
118    
119            * R/triangularMatrix.R (isTriangular): methods for all subclasses
120            instead of "triangularMatrix" -- just to disambiguate
121    
122    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
125            * tests/indexing.R: example that fails above
126    
127    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
130            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
131                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
132    
133            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
134            * src/Tsparse.h, init.c: ditto
135            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
136                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
137            * R/sparseMatrix.R (isTriangular): hence simplified
138    
139    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/Ops.R (.Arith.Csparse): new utility factored out of former
142              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
143    
144    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
147    
148            * inst/test-tools.R (isOrthogonal): new function; also file restructured
149    
150    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
153            coercion to "nMatrix" and "pMatrix"
154    
155            * R/AllClass.R: "Schur" class;  "number" class union
156            * man/number-class.Rd:
157            * man/Schur-class.Rd:
158    
159            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
160            (.simpleSchur): Schur() method for diagonal matrices
161            (.triSchur):    Schur() method for triangular matrices
162            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
163    
164    
165    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
168    
169    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
172                    in order to ensure 'system = *' is not lost;
173                    formals()$system instead of cut&paste.
174            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
175    
176    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * DESCRIPTION (Date): make ready for release --> 0.999375-4
179    
180            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
181    
182    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
185                    and hence does as.vector(.).
186            * man/pMatrix-class.Rd: docs
187            * R/sparseMatrix.R: fix for printing "integer sparse"
188    
189            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
190    
191            * R/Matrix.R and others: use "exact" function argument list for
192                    both "["   : (x, i,j, ..., drop)
193                    and  "[<-" : (x, i,j, ..., value)
194    
195            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
196            * R/Tsparse.R (replTmat):    ditto
197            * R/diagMatrix.R (replDiag): ditto
198            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
199            * tests/indexing.R: testing the above
200    
201    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/sparseMatrix.R (cov2cor): method for sparse matrices
204    
205            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
206    
207            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
208    
209            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
210    
211    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/Matrix.R: "generic" cov2cor() method
214    
215            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
216                    speed up Q %*% D %*% t(Q)
217            * tests/dpoMatrix.R: test nearPD()
218    
219    2007-12-05  Doug Bates and Martin Maechler
220    
221            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
222            stats::xtabs() allowing to create sparse matrices.
223    
224    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
227    
228    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
231    
232    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/LU.R: solve() method for "denseLU"
235    
236    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * DESCRIPTION (Version): 0.999375-3 preparing for release
239    
240            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
241    
242            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
243    
244    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
247              thanks to Kasper Kristensen.
248            * tests/matprod.R: regression test for that.
249    
250    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
251    
252            * [r4778] R/AllGeneric.R: Check R version before defining generics for
253              primitives
254    
255    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * R/denseMatrix.R (rcond): method
258            * R/sparseQR.R (rcond): method, use x or t(x)
259    
260    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
263            matrices.
264            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
265    
266            * man/rcond.Rd: mention the more general definition, and add
267            example for non-square matrices.
268    
269            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
270    
271    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
274    
275    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
278            * tests/indexing.R: add new regression for the above cases.
279    
280    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * src/Mutils.h (__sun): clause for alloca.h on Solaris
283    
284    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * DESCRIPTION (Date, Version): 0.999375-2
287    
288    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/HBMM.R (readMM): make work for pattern matrices as well
291    
292    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
293    
294            * [r4730] src/Mutils.h: declare alloca
295            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
296              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
297              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
298              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
299              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
300              methods; switch writeMM to use CHOLMOD code; repair readMM
301    
302    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
305            Oehlschlaegel's ... result type still to be discussed!
306    
307    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * man/image-methods.Rd: new, combining all image() methods
310    
311    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
314            to work via dgC...
315    
316            * R/Matrix.R (Matrix): special treatment for "table" (S3)
317    
318    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/dgTMatrix.R (image): change defaults to
321                    aspect = "iso", colorkey = FALSE
322    
323    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
326            must copy its *expanded* x slot before LAPACK call.
327    
328            * tests/matprod.R: test the last days' changes.
329    
330    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
331    
332            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
333              as well as in sources
334            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
335              Lapack call
336    
337    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
340                    ("Matrix", "matrix") which is needed in some cases.
341            Ditto for solve().
342    
343            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
344            infinite recursion in dispatch for some cases.
345    
346    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
347    
348            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
349              so pointers match
350    
351    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * DESCRIPTION (Date): set ready for release -- 0.999375-1
354    
355    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
356    
357            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
358              src/chm_common.c, src/chm_common.h: Change API for
359              numeric_as_chm_dense and N_AS_CHM_DN
360    
361    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
364            * tests/matprod.R: regr.test for it
365    
366    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
369            * tests/group-methods.R: and regression-test it
370    
371    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
372    
373            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
374              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
375              triplet_to_sparse, documentation, use typedefs
376    
377  2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379          * man/dpoMatrix-class.Rd: added 'corMatrix' example          * man/dpoMatrix-class.Rd: added 'corMatrix' example

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