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revision 2011, Fri Jul 20 12:56:10 2007 UTC revision 2128, Thu Mar 13 23:08:34 2008 UTC
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1    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
4    
5            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
6              <diagonal> o <sparse_triangular>
7              setAs(., "nMatrix") added.
8    
9            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
10    
11            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
12                    new argument 'checkDense = FALSE'.
13    
14    
15    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
18            back-permutation of the matrix exponential.
19    
20            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
21    
22            * DESCRIPTION (Date,Version): ready to release 0.999375-5
23    
24            * tests/simple.R: testing diagN2U
25    
26    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/Auxiliaries.R (diagN2U): interface to
29    
30            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
31    
32            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
33    
34    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * src/chm_common.c (chm_diagN2U): new utility.
37    
38            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
39            make use of chm_diagN2U() and hence now preserve triangularity and
40            unit-triangularity.
41    
42            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
43    
44    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
47    
48            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
49            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
50    
51            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
52    
53            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
54    
55            * src/chm_common.c (AS_CHM_FINISH): add note about problem
56            for triangular (diag = "U").
57    
58    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
61            * R/bind.R:  .Call(dense_to_Csparse, *)
62    
63    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/Matrix.R (Matrix): no longer use coercions to specific classes
66                    (since we are discouraging them in user code).
67    
68            * tests/*.R: also replaces coercions to specific classes by
69            coercions to super classes.
70    
71            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
72    
73    
74    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
77    
78            * src/dense.c (dense_band): generalized from ddense_band
79    
80            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
81              now for "denseMatrix" (instead of just "ddense*"); much
82              simplified setMethod()s for these.
83    
84            * src/dense.c (dense_to_symmetric): generalized from ddense_*
85    
86    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
89            version of as(*, "symmetricMatric").
90    
91            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
92            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
93    
94    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/Matrix.R (subset.ij): utility, as first step to faster
97               M [ <ij-matrix> ] indexing.
98    
99            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
100    
101            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
102            for more efficient symmpart() and skewpart() methods.
103    
104            * src/Mutils.c (equal_string_vectors): utility
105    
106            * src/dense.c (ddense_to_symmetric): new function used in
107    
108            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
109    
110            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
111            order to match the generic (and evade .local(..)).
112    
113            * R/dsCMatrix.R: dgC -> dsC: use C code!
114    
115            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
116            as per TODO
117    
118            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
119    
120            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
121    
122    
123    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
126    
127            * R/Auxiliaries.R (non0.i): take out of non0ind
128    
129            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
130            make tril(), triu(), band() work for "matrix" and all "dense*"
131    
132            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
133            * tests/simple.R: test the fix above
134    
135            * R/sparseMatrix.R ([): simplification: no coerce to <general>
136                    before we use as(., <Tsparse>)[...] anyway
137    
138            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
139    
140            * R/triangularMatrix.R (isTriangular): methods for all subclasses
141            instead of "triangularMatrix" -- just to disambiguate
142    
143    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
146            * tests/indexing.R: example that fails above
147    
148    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
151            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
152                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
153    
154            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
155            * src/Tsparse.h, init.c: ditto
156            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
157                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
158            * R/sparseMatrix.R (isTriangular): hence simplified
159    
160    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/Ops.R (.Arith.Csparse): new utility factored out of former
163              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
164    
165    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
168    
169            * inst/test-tools.R (isOrthogonal): new function; also file restructured
170    
171    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
174            coercion to "nMatrix" and "pMatrix"
175    
176            * R/AllClass.R: "Schur" class;  "number" class union
177            * man/number-class.Rd:
178            * man/Schur-class.Rd:
179    
180            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
181            (.simpleSchur): Schur() method for diagonal matrices
182            (.triSchur):    Schur() method for triangular matrices
183            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
184    
185    
186    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
189    
190    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
193                    in order to ensure 'system = *' is not lost;
194                    formals()$system instead of cut&paste.
195            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
196    
197    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * DESCRIPTION (Date): make ready for release --> 0.999375-4
200    
201            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
202    
203    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
206                    and hence does as.vector(.).
207            * man/pMatrix-class.Rd: docs
208            * R/sparseMatrix.R: fix for printing "integer sparse"
209    
210            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
211    
212            * R/Matrix.R and others: use "exact" function argument list for
213                    both "["   : (x, i,j, ..., drop)
214                    and  "[<-" : (x, i,j, ..., value)
215    
216            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
217            * R/Tsparse.R (replTmat):    ditto
218            * R/diagMatrix.R (replDiag): ditto
219            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
220            * tests/indexing.R: testing the above
221    
222    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/sparseMatrix.R (cov2cor): method for sparse matrices
225    
226            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
227    
228            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
229    
230            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
231    
232    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/Matrix.R: "generic" cov2cor() method
235    
236            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
237                    speed up Q %*% D %*% t(Q)
238            * tests/dpoMatrix.R: test nearPD()
239    
240    2007-12-05  Doug Bates and Martin Maechler
241    
242            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
243            stats::xtabs() allowing to create sparse matrices.
244    
245    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
248    
249    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
252    
253    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * R/LU.R: solve() method for "denseLU"
256    
257    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * DESCRIPTION (Version): 0.999375-3 preparing for release
260    
261            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
262    
263            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
264    
265    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
268              thanks to Kasper Kristensen.
269            * tests/matprod.R: regression test for that.
270    
271    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
272    
273            * [r4778] R/AllGeneric.R: Check R version before defining generics for
274              primitives
275    
276    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/denseMatrix.R (rcond): method
279            * R/sparseQR.R (rcond): method, use x or t(x)
280    
281    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
284            matrices.
285            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
286    
287            * man/rcond.Rd: mention the more general definition, and add
288            example for non-square matrices.
289    
290            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
291    
292    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
295    
296    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
299            * tests/indexing.R: add new regression for the above cases.
300    
301    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * src/Mutils.h (__sun): clause for alloca.h on Solaris
304    
305    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * DESCRIPTION (Date, Version): 0.999375-2
308    
309    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/HBMM.R (readMM): make work for pattern matrices as well
312    
313    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
314    
315            * [r4730] src/Mutils.h: declare alloca
316            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
317              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
318              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
319              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
320              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
321              methods; switch writeMM to use CHOLMOD code; repair readMM
322    
323    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
326            Oehlschlaegel's ... result type still to be discussed!
327    
328    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * man/image-methods.Rd: new, combining all image() methods
331    
332    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
335            to work via dgC...
336    
337            * R/Matrix.R (Matrix): special treatment for "table" (S3)
338    
339    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/dgTMatrix.R (image): change defaults to
342                    aspect = "iso", colorkey = FALSE
343    
344    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
347            must copy its *expanded* x slot before LAPACK call.
348    
349            * tests/matprod.R: test the last days' changes.
350    
351    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
352    
353            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
354              as well as in sources
355            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
356              Lapack call
357    
358    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
361                    ("Matrix", "matrix") which is needed in some cases.
362            Ditto for solve().
363    
364            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
365            infinite recursion in dispatch for some cases.
366    
367    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
368    
369            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
370              so pointers match
371    
372    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * DESCRIPTION (Date): set ready for release -- 0.999375-1
375    
376    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
377    
378            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
379              src/chm_common.c, src/chm_common.h: Change API for
380              numeric_as_chm_dense and N_AS_CHM_DN
381    
382    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
385            * tests/matprod.R: regr.test for it
386    
387  2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389          * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")          * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")

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