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revision 2105, Tue Jan 15 10:16:29 2008 UTC revision 2199, Mon Jun 2 16:09:12 2008 UTC
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1    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
4    
5            * R/not.R: fix !<ldiMatrix>
6            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
7    
8            * R/diagMatrix.R (Ops): fix one-off thinko in
9            <diagonal> o <numeric> methods
10    
11            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
12    
13    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
16            * tests/Simple.R: testing the above
17    
18    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
21    
22    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
25            * NAMESPACE (unname): finally exported
26    
27    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/Auxiliaries.R (cholMat): possibly keep packed
30    
31            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
32            for R < 2.7.0.
33    
34            * R/Tsparse.R ([): for triangularMatrix, check if result may be
35            triangular.
36            * tests/indexing.R: regression test
37    
38    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
41            * R/Ops.R: more methods, for lMatrix/nMatrix
42    
43    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/expm.R: new file for all expm() methods; notably new ones for
46            diagonal*, triangular*, symmetric* and also simple "matrix".
47    
48    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
51    
52            * inst/test-tools.R (assert.EQ.mat): better message when not equal
53    
54            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
55    
56            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
57            [dl]denseMatrix {identical slots; but more logical method dispatch}
58    
59    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
62    
63            * R/diagMatrix.R (determinant): method
64    
65    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
68    
69            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
70    
71            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
72            its diagonal
73    
74    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
77    
78            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
79    
80            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
81    
82            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
83    
84    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
87    
88            * R/Ops.R (.do.Logic.lsparse): fix NA case
89    
90            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
91    
92            * R/Auxiliaries.R (nnzero): fix special cases, using
93            * R/Auxiliaries.R (indDiag): new utility
94            * R/Auxiliaries.R (indTri): new argument 'diag'
95    
96            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
97    
98    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
101    
102            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
103            ".tCMatrix" triangular matrix.
104    
105            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
106            'clx' can be class *or* class representation.
107            (nnzSparse): new.
108            (non0ind): new 'xtendSymm' argument; used in
109            * R/Ops.R:
110    
111            * R/pMatrix.R: more efficient determinant() method
112    
113    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
116            * [disactivated] NAMESPACE: export(det)
117    
118            * R/diagMatrix.R (mkDiag): new substitute for diag()
119    
120            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
121            (as0, as1): new utility.
122    
123            * R/Csparse.R (diag, band): need diagU2N()
124    
125            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
126    
127            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
128    
129            * R/Ops.R (Compare): fix <nsp> o <nsp> case
130    
131            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
132    
133    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/Auxiliaries.R (signPerm): new utility for
136            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
137    
138            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
139            since we have our own error handler (and can use tryCatch() from R).
140    
141    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
144    
145            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
146            when not positive definite.
147    
148            * R/Auxiliaries.R (asTri): new auxiliary
149            (non0.i): make *much* faster for Tsparse with many non-zero
150            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
151    
152            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
153            test-tools.R , see below
154    
155            * R/dMatrix.R: fix "Summary" method: + diagU2N()
156    
157            * NAMESPACE, R/Matrix.R: add mean() method
158    
159    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
162            cold-hot colors; try *changed* default useAbs = FALSE
163            * man/image-methods.Rd:  nice examples
164    
165    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * inst/test-tools.R (checkMatrix): new function for modularizing part
168            of tstMatrixClass() in tests/Class+Meth.R
169    
170            * R/dsCMatrix.R: coercion from "matrix"
171            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
172    
173            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
174            add test for as(matrix(,0,0), <class>)
175    
176    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
179            work as determinant(matrix(,0,0)).
180    
181            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
182            * man/sparseLU-class.Rd: ditto
183    
184            * R/dgCMatrix.R (determinant): method building on lu()
185            * R/sparseMatrix.R, Matrix.R, ...: ditto
186    
187            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
188    
189    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
192            pattern matrices.
193    
194    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * src/dense.c (dense_to_Csparse): all declarations *before*
197            R_CheckStack(); needed e.g. for ancient gcc 2.96.
198    
199    
200    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * DESCRIPTION (Version): 0.999375-9 --- need to release
203            for R-devel (and R 2.7.0 alpha soon).
204    
205            * R/AllClass.R: drop "double" from "atomicVector" class union
206    
207            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
208            * R/dgeMatrix.R: ditto
209    
210            * R/sparseMatrix.R (summary): count NAs
211    
212            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
213    
214    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
217            order to become compatible to new R 2.7.0 base::rcond().
218    
219    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
222    
223            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
224    
225            * inst/test-tools.R (isValid): new utility, used much in
226            * tests/simple.R:
227    
228            * man/BunchKaufman-methods.Rd: added too
229    
230    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/dsyMatrix.R: add BunchKaufman() methods.
233            * R/dspMatrix.R:
234    
235            * src/init.c: add dsyMatrix_trf
236    
237    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
238    
239            * DESCRIPTION (Version): release 0.999375-7
240            * src/CHMfactor.c (CHMfactor_update): fix
241    
242    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
245            internal_chm_factor().
246    
247            * R/AllGeneric.R: do *not* define a "chol" generic
248                    (but rather use the implicit one *without* making pivot
249                    part of the signature)
250            * R/*.R: drop the 'pivot' from chol's signature and make
251                    'pivot=FALSE' a default argument of method definitions.
252    
253            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
254            version of Matrix
255    
256    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
259    
260            * R/sparseMatrix.R (is.na): new simple method
261            * R/denseMatrix.R (is.na): ditto.
262    
263            * R/diagMatrix.R (.symDiagonal): newly exported utility.
264    
265            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
266    
267            * src/UFsparse_download.sh: -->
268            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
269    
270    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
273            functionality; barely tested in
274            * tests/factorizing.R
275    
276            * src/Csparse.c (diag_tC): new functionality to enable faster
277            determinant(<dsCMatrix>, .) in
278            * R/dsCMatrix.R
279    
280    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
281    
282            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
283              src/CHMfactor.c, src/CHMfactor.h,
284              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
285              Log-determinant of the parent matrix from a CHMfactor object as
286              chm_factor_ldetL2; documentation and support
287    
288    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
291    
292    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
295            warning.
296    
297    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
300    
301            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
302              <diagonal> o <sparse_triangular>
303              setAs(., "nMatrix") added.
304    
305            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
306    
307            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
308                    new argument 'checkDense = FALSE'.
309    
310    
311    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
314            back-permutation of the matrix exponential.
315    
316            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
317    
318            * DESCRIPTION (Date,Version): ready to release 0.999375-5
319    
320            * tests/simple.R: testing diagN2U
321    
322    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/Auxiliaries.R (diagN2U): interface to
325    
326            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
327    
328            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
329    
330    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * src/chm_common.c (chm_diagN2U): new utility.
333    
334            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
335            make use of chm_diagN2U() and hence now preserve triangularity and
336            unit-triangularity.
337    
338            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
339    
340    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
343    
344            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
345            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
346    
347            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
348    
349            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
350    
351            * src/chm_common.c (AS_CHM_FINISH): add note about problem
352            for triangular (diag = "U").
353    
354    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
357            * R/bind.R:  .Call(dense_to_Csparse, *)
358    
359    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/Matrix.R (Matrix): no longer use coercions to specific classes
362                    (since we are discouraging them in user code).
363    
364            * tests/*.R: also replaces coercions to specific classes by
365            coercions to super classes.
366    
367            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
368    
369    
370    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
373    
374            * src/dense.c (dense_band): generalized from ddense_band
375    
376            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
377              now for "denseMatrix" (instead of just "ddense*"); much
378              simplified setMethod()s for these.
379    
380            * src/dense.c (dense_to_symmetric): generalized from ddense_*
381    
382    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
385            version of as(*, "symmetricMatric").
386    
387            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
388            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
389    
390    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * R/Matrix.R (subset.ij): utility, as first step to faster
393               M [ <ij-matrix> ] indexing.
394    
395            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
396    
397            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
398            for more efficient symmpart() and skewpart() methods.
399    
400            * src/Mutils.c (equal_string_vectors): utility
401    
402            * src/dense.c (ddense_to_symmetric): new function used in
403    
404            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
405    
406            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
407            order to match the generic (and evade .local(..)).
408    
409            * R/dsCMatrix.R: dgC -> dsC: use C code!
410    
411            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
412            as per TODO
413    
414            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
415    
416            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
417    
418    
419    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
422    
423            * R/Auxiliaries.R (non0.i): take out of non0ind
424    
425            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
426            make tril(), triu(), band() work for "matrix" and all "dense*"
427    
428            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
429            * tests/simple.R: test the fix above
430    
431            * R/sparseMatrix.R ([): simplification: no coerce to <general>
432                    before we use as(., <Tsparse>)[...] anyway
433    
434            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
435    
436            * R/triangularMatrix.R (isTriangular): methods for all subclasses
437            instead of "triangularMatrix" -- just to disambiguate
438    
439    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
442            * tests/indexing.R: example that fails above
443    
444    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
447            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
448                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
449    
450            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
451            * src/Tsparse.h, init.c: ditto
452            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
453                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
454            * R/sparseMatrix.R (isTriangular): hence simplified
455    
456    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * R/Ops.R (.Arith.Csparse): new utility factored out of former
459              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
460    
461    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
464    
465            * inst/test-tools.R (isOrthogonal): new function; also file restructured
466    
467    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
470            coercion to "nMatrix" and "pMatrix"
471    
472            * R/AllClass.R: "Schur" class;  "number" class union
473            * man/number-class.Rd:
474            * man/Schur-class.Rd:
475    
476            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
477            (.simpleSchur): Schur() method for diagonal matrices
478            (.triSchur):    Schur() method for triangular matrices
479            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
480    
481    
482    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
485    
486  2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488          * 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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