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revision 2105, Tue Jan 15 10:16:29 2008 UTC revision 2194, Tue May 20 06:44:19 2008 UTC
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1    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
4    
5    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
8            * NAMESPACE (unname): finally exported
9    
10    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/Auxiliaries.R (cholMat): possibly keep packed
13    
14            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
15            for R < 2.7.0.
16    
17            * R/Tsparse.R ([): for triangularMatrix, check if result may be
18            triangular.
19            * tests/indexing.R: regression test
20    
21    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
24            * R/Ops.R: more methods, for lMatrix/nMatrix
25    
26    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/expm.R: new file for all expm() methods; notably new ones for
29            diagonal*, triangular*, symmetric* and also simple "matrix".
30    
31    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
34    
35            * inst/test-tools.R (assert.EQ.mat): better message when not equal
36    
37            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
38    
39            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
40            [dl]denseMatrix {identical slots; but more logical method dispatch}
41    
42    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
45    
46            * R/diagMatrix.R (determinant): method
47    
48    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
51    
52            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
53    
54            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
55            its diagonal
56    
57    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
60    
61            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
62    
63            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
64    
65            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
66    
67    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
70    
71            * R/Ops.R (.do.Logic.lsparse): fix NA case
72    
73            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
74    
75            * R/Auxiliaries.R (nnzero): fix special cases, using
76            * R/Auxiliaries.R (indDiag): new utility
77            * R/Auxiliaries.R (indTri): new argument 'diag'
78    
79            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
80    
81    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
84    
85            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
86            ".tCMatrix" triangular matrix.
87    
88            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
89            'clx' can be class *or* class representation.
90            (nnzSparse): new.
91            (non0ind): new 'xtendSymm' argument; used in
92            * R/Ops.R:
93    
94            * R/pMatrix.R: more efficient determinant() method
95    
96    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
99            * [disactivated] NAMESPACE: export(det)
100    
101            * R/diagMatrix.R (mkDiag): new substitute for diag()
102    
103            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
104            (as0, as1): new utility.
105    
106            * R/Csparse.R (diag, band): need diagU2N()
107    
108            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
109    
110            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
111    
112            * R/Ops.R (Compare): fix <nsp> o <nsp> case
113    
114            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
115    
116    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Auxiliaries.R (signPerm): new utility for
119            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
120    
121            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
122            since we have our own error handler (and can use tryCatch() from R).
123    
124    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
127    
128            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
129            when not positive definite.
130    
131            * R/Auxiliaries.R (asTri): new auxiliary
132            (non0.i): make *much* faster for Tsparse with many non-zero
133            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
134    
135            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
136            test-tools.R , see below
137    
138            * R/dMatrix.R: fix "Summary" method: + diagU2N()
139    
140            * NAMESPACE, R/Matrix.R: add mean() method
141    
142    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
145            cold-hot colors; try *changed* default useAbs = FALSE
146            * man/image-methods.Rd:  nice examples
147    
148    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * inst/test-tools.R (checkMatrix): new function for modularizing part
151            of tstMatrixClass() in tests/Class+Meth.R
152    
153            * R/dsCMatrix.R: coercion from "matrix"
154            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
155    
156            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
157            add test for as(matrix(,0,0), <class>)
158    
159    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
162            work as determinant(matrix(,0,0)).
163    
164            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
165            * man/sparseLU-class.Rd: ditto
166    
167            * R/dgCMatrix.R (determinant): method building on lu()
168            * R/sparseMatrix.R, Matrix.R, ...: ditto
169    
170            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
171    
172    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
175            pattern matrices.
176    
177    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * src/dense.c (dense_to_Csparse): all declarations *before*
180            R_CheckStack(); needed e.g. for ancient gcc 2.96.
181    
182    
183    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * DESCRIPTION (Version): 0.999375-9 --- need to release
186            for R-devel (and R 2.7.0 alpha soon).
187    
188            * R/AllClass.R: drop "double" from "atomicVector" class union
189    
190            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
191            * R/dgeMatrix.R: ditto
192    
193            * R/sparseMatrix.R (summary): count NAs
194    
195            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
196    
197    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
200            order to become compatible to new R 2.7.0 base::rcond().
201    
202    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
205    
206            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
207    
208            * inst/test-tools.R (isValid): new utility, used much in
209            * tests/simple.R:
210    
211            * man/BunchKaufman-methods.Rd: added too
212    
213    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/dsyMatrix.R: add BunchKaufman() methods.
216            * R/dspMatrix.R:
217    
218            * src/init.c: add dsyMatrix_trf
219    
220    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
221    
222            * DESCRIPTION (Version): release 0.999375-7
223            * src/CHMfactor.c (CHMfactor_update): fix
224    
225    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
228            internal_chm_factor().
229    
230            * R/AllGeneric.R: do *not* define a "chol" generic
231                    (but rather use the implicit one *without* making pivot
232                    part of the signature)
233            * R/*.R: drop the 'pivot' from chol's signature and make
234                    'pivot=FALSE' a default argument of method definitions.
235    
236            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
237            version of Matrix
238    
239    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
242    
243            * R/sparseMatrix.R (is.na): new simple method
244            * R/denseMatrix.R (is.na): ditto.
245    
246            * R/diagMatrix.R (.symDiagonal): newly exported utility.
247    
248            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
249    
250            * src/UFsparse_download.sh: -->
251            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
252    
253    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
256            functionality; barely tested in
257            * tests/factorizing.R
258    
259            * src/Csparse.c (diag_tC): new functionality to enable faster
260            determinant(<dsCMatrix>, .) in
261            * R/dsCMatrix.R
262    
263    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
264    
265            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
266              src/CHMfactor.c, src/CHMfactor.h,
267              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
268              Log-determinant of the parent matrix from a CHMfactor object as
269              chm_factor_ldetL2; documentation and support
270    
271    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
274    
275    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
278            warning.
279    
280    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
283    
284            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
285              <diagonal> o <sparse_triangular>
286              setAs(., "nMatrix") added.
287    
288            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
289    
290            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
291                    new argument 'checkDense = FALSE'.
292    
293    
294    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
297            back-permutation of the matrix exponential.
298    
299            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
300    
301            * DESCRIPTION (Date,Version): ready to release 0.999375-5
302    
303            * tests/simple.R: testing diagN2U
304    
305    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/Auxiliaries.R (diagN2U): interface to
308    
309            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
310    
311            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
312    
313    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * src/chm_common.c (chm_diagN2U): new utility.
316    
317            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
318            make use of chm_diagN2U() and hence now preserve triangularity and
319            unit-triangularity.
320    
321            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
322    
323    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
326    
327            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
328            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
329    
330            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
331    
332            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
333    
334            * src/chm_common.c (AS_CHM_FINISH): add note about problem
335            for triangular (diag = "U").
336    
337    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
340            * R/bind.R:  .Call(dense_to_Csparse, *)
341    
342    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * R/Matrix.R (Matrix): no longer use coercions to specific classes
345                    (since we are discouraging them in user code).
346    
347            * tests/*.R: also replaces coercions to specific classes by
348            coercions to super classes.
349    
350            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
351    
352    
353    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
356    
357            * src/dense.c (dense_band): generalized from ddense_band
358    
359            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
360              now for "denseMatrix" (instead of just "ddense*"); much
361              simplified setMethod()s for these.
362    
363            * src/dense.c (dense_to_symmetric): generalized from ddense_*
364    
365    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
368            version of as(*, "symmetricMatric").
369    
370            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
371            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
372    
373    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/Matrix.R (subset.ij): utility, as first step to faster
376               M [ <ij-matrix> ] indexing.
377    
378            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
379    
380            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
381            for more efficient symmpart() and skewpart() methods.
382    
383            * src/Mutils.c (equal_string_vectors): utility
384    
385            * src/dense.c (ddense_to_symmetric): new function used in
386    
387            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
388    
389            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
390            order to match the generic (and evade .local(..)).
391    
392            * R/dsCMatrix.R: dgC -> dsC: use C code!
393    
394            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
395            as per TODO
396    
397            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
398    
399            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
400    
401    
402    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
405    
406            * R/Auxiliaries.R (non0.i): take out of non0ind
407    
408            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
409            make tril(), triu(), band() work for "matrix" and all "dense*"
410    
411            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
412            * tests/simple.R: test the fix above
413    
414            * R/sparseMatrix.R ([): simplification: no coerce to <general>
415                    before we use as(., <Tsparse>)[...] anyway
416    
417            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
418    
419            * R/triangularMatrix.R (isTriangular): methods for all subclasses
420            instead of "triangularMatrix" -- just to disambiguate
421    
422    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
425            * tests/indexing.R: example that fails above
426    
427    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
430            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
431                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
432    
433            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
434            * src/Tsparse.h, init.c: ditto
435            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
436                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
437            * R/sparseMatrix.R (isTriangular): hence simplified
438    
439    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/Ops.R (.Arith.Csparse): new utility factored out of former
442              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
443    
444    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
447    
448            * inst/test-tools.R (isOrthogonal): new function; also file restructured
449    
450    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
453            coercion to "nMatrix" and "pMatrix"
454    
455            * R/AllClass.R: "Schur" class;  "number" class union
456            * man/number-class.Rd:
457            * man/Schur-class.Rd:
458    
459            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
460            (.simpleSchur): Schur() method for diagonal matrices
461            (.triSchur):    Schur() method for triangular matrices
462            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
463    
464    
465    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
468    
469  2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471          * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"          * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"

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