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revision 2011, Fri Jul 20 12:56:10 2007 UTC revision 2144, Tue Mar 18 23:08:12 2008 UTC
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1    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
4    
5            * R/sparseMatrix.R (is.na): new simple method
6            * R/denseMatrix.R (is.na): ditto.
7    
8            * R/diagMatrix.R (.symDiagonal): newly exported utility.
9    
10            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
11    
12            * src/UFsparse_download.sh: -->
13            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
14    
15    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
18            functionality; barely tested in
19            * tests/factorizing.R
20    
21            * src/Csparse.c (diag_tC): new functionality to enable faster
22            determinant(<dsCMatrix>, .) in
23            * R/dsCMatrix.R
24    
25    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
26    
27            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
28              src/CHMfactor.c, src/CHMfactor.h,
29              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
30              Log-determinant of the parent matrix from a CHMfactor object as
31              chm_factor_ldetL2; documentation and support
32    
33    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
36    
37    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
40            warning.
41    
42    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
45    
46            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
47              <diagonal> o <sparse_triangular>
48              setAs(., "nMatrix") added.
49    
50            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
51    
52            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
53                    new argument 'checkDense = FALSE'.
54    
55    
56    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
59            back-permutation of the matrix exponential.
60    
61            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
62    
63            * DESCRIPTION (Date,Version): ready to release 0.999375-5
64    
65            * tests/simple.R: testing diagN2U
66    
67    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/Auxiliaries.R (diagN2U): interface to
70    
71            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
72    
73            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
74    
75    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * src/chm_common.c (chm_diagN2U): new utility.
78    
79            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
80            make use of chm_diagN2U() and hence now preserve triangularity and
81            unit-triangularity.
82    
83            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
84    
85    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
88    
89            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
90            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
91    
92            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
93    
94            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
95    
96            * src/chm_common.c (AS_CHM_FINISH): add note about problem
97            for triangular (diag = "U").
98    
99    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
102            * R/bind.R:  .Call(dense_to_Csparse, *)
103    
104    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * R/Matrix.R (Matrix): no longer use coercions to specific classes
107                    (since we are discouraging them in user code).
108    
109            * tests/*.R: also replaces coercions to specific classes by
110            coercions to super classes.
111    
112            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
113    
114    
115    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
118    
119            * src/dense.c (dense_band): generalized from ddense_band
120    
121            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
122              now for "denseMatrix" (instead of just "ddense*"); much
123              simplified setMethod()s for these.
124    
125            * src/dense.c (dense_to_symmetric): generalized from ddense_*
126    
127    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
130            version of as(*, "symmetricMatric").
131    
132            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
133            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
134    
135    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/Matrix.R (subset.ij): utility, as first step to faster
138               M [ <ij-matrix> ] indexing.
139    
140            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
141    
142            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
143            for more efficient symmpart() and skewpart() methods.
144    
145            * src/Mutils.c (equal_string_vectors): utility
146    
147            * src/dense.c (ddense_to_symmetric): new function used in
148    
149            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
150    
151            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
152            order to match the generic (and evade .local(..)).
153    
154            * R/dsCMatrix.R: dgC -> dsC: use C code!
155    
156            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
157            as per TODO
158    
159            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
160    
161            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
162    
163    
164    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
167    
168            * R/Auxiliaries.R (non0.i): take out of non0ind
169    
170            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
171            make tril(), triu(), band() work for "matrix" and all "dense*"
172    
173            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
174            * tests/simple.R: test the fix above
175    
176            * R/sparseMatrix.R ([): simplification: no coerce to <general>
177                    before we use as(., <Tsparse>)[...] anyway
178    
179            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
180    
181            * R/triangularMatrix.R (isTriangular): methods for all subclasses
182            instead of "triangularMatrix" -- just to disambiguate
183    
184    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
187            * tests/indexing.R: example that fails above
188    
189    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
192            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
193                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
194    
195            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
196            * src/Tsparse.h, init.c: ditto
197            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
198                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
199            * R/sparseMatrix.R (isTriangular): hence simplified
200    
201    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/Ops.R (.Arith.Csparse): new utility factored out of former
204              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
205    
206    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
209    
210            * inst/test-tools.R (isOrthogonal): new function; also file restructured
211    
212    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
215            coercion to "nMatrix" and "pMatrix"
216    
217            * R/AllClass.R: "Schur" class;  "number" class union
218            * man/number-class.Rd:
219            * man/Schur-class.Rd:
220    
221            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
222            (.simpleSchur): Schur() method for diagonal matrices
223            (.triSchur):    Schur() method for triangular matrices
224            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
225    
226    
227    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
230    
231    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
234                    in order to ensure 'system = *' is not lost;
235                    formals()$system instead of cut&paste.
236            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
237    
238    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * DESCRIPTION (Date): make ready for release --> 0.999375-4
241    
242            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
243    
244    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
247                    and hence does as.vector(.).
248            * man/pMatrix-class.Rd: docs
249            * R/sparseMatrix.R: fix for printing "integer sparse"
250    
251            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
252    
253            * R/Matrix.R and others: use "exact" function argument list for
254                    both "["   : (x, i,j, ..., drop)
255                    and  "[<-" : (x, i,j, ..., value)
256    
257            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
258            * R/Tsparse.R (replTmat):    ditto
259            * R/diagMatrix.R (replDiag): ditto
260            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
261            * tests/indexing.R: testing the above
262    
263    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/sparseMatrix.R (cov2cor): method for sparse matrices
266    
267            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
268    
269            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
270    
271            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
272    
273    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/Matrix.R: "generic" cov2cor() method
276    
277            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
278                    speed up Q %*% D %*% t(Q)
279            * tests/dpoMatrix.R: test nearPD()
280    
281    2007-12-05  Doug Bates and Martin Maechler
282    
283            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
284            stats::xtabs() allowing to create sparse matrices.
285    
286    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
289    
290    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
293    
294    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/LU.R: solve() method for "denseLU"
297    
298    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * DESCRIPTION (Version): 0.999375-3 preparing for release
301    
302            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
303    
304            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
305    
306    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
309              thanks to Kasper Kristensen.
310            * tests/matprod.R: regression test for that.
311    
312    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
313    
314            * [r4778] R/AllGeneric.R: Check R version before defining generics for
315              primitives
316    
317    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/denseMatrix.R (rcond): method
320            * R/sparseQR.R (rcond): method, use x or t(x)
321    
322    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
325            matrices.
326            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
327    
328            * man/rcond.Rd: mention the more general definition, and add
329            example for non-square matrices.
330    
331            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
332    
333    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
336    
337    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
340            * tests/indexing.R: add new regression for the above cases.
341    
342    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * src/Mutils.h (__sun): clause for alloca.h on Solaris
345    
346    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * DESCRIPTION (Date, Version): 0.999375-2
349    
350    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/HBMM.R (readMM): make work for pattern matrices as well
353    
354    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
355    
356            * [r4730] src/Mutils.h: declare alloca
357            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
358              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
359              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
360              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
361              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
362              methods; switch writeMM to use CHOLMOD code; repair readMM
363    
364    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
367            Oehlschlaegel's ... result type still to be discussed!
368    
369    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * man/image-methods.Rd: new, combining all image() methods
372    
373    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
376            to work via dgC...
377    
378            * R/Matrix.R (Matrix): special treatment for "table" (S3)
379    
380    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/dgTMatrix.R (image): change defaults to
383                    aspect = "iso", colorkey = FALSE
384    
385    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
388            must copy its *expanded* x slot before LAPACK call.
389    
390            * tests/matprod.R: test the last days' changes.
391    
392    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
393    
394            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
395              as well as in sources
396            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
397              Lapack call
398    
399    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
402                    ("Matrix", "matrix") which is needed in some cases.
403            Ditto for solve().
404    
405            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
406            infinite recursion in dispatch for some cases.
407    
408    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
409    
410            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
411              so pointers match
412    
413    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * DESCRIPTION (Date): set ready for release -- 0.999375-1
416    
417    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
418    
419            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
420              src/chm_common.c, src/chm_common.h: Change API for
421              numeric_as_chm_dense and N_AS_CHM_DN
422    
423    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
426            * tests/matprod.R: regr.test for it
427    
428  2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430          * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")          * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")

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