SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1922, Sat Jun 23 18:08:48 2007 UTC revision 2227, Mon Jul 21 19:49:33 2008 UTC
# Line 1  Line 1 
1    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
4            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
5            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
6            diagU2N().
7    
8    
9            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
10            .spDiagonal() and new .trDiagonal().
11    
12            * R/dtCMatrix.R (solve): make use of .trDiagonal()
13    
14    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
17            stumbled upon by Michael H.
18    
19            * tests/validObj.R: testing the bug-fix
20    
21            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
22            versions.
23    
24            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
25            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
26    
27            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
28              AS_CHM_SP() which includes diagU2N.
29    
30            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
31            adapt to 3 arguments.
32    
33    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
34    
35            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
36              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
37              new solve method
38            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
39              Csparse_diagU2N functionality into Matrix_as_cs
40    
41    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * [r2215] inst/doc/factor2sparse.Rnw: revive a year-old unfinished
44              vignette
45            * [r2214] R/AllGeneric.R: cosmetic
46            * [r2213] man/image-methods.Rd: typo ("non-number" :-\ )
47    
48    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
49    
50            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
51              argument with default TRUE
52            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
53              Csparse_diagU2N
54            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
55              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
56              parent array; new solve method for signature(a = "dtCMatrix", b =
57              "sparseMatrix")
58    
59    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/diagMatrix.R (.bdiag): also keep triangular
62            * [r2209] ChangeLog, DESCRIPTION, R/diagMatrix.R, inst/test-tools.R,
63              man/dsCMatrix-class.Rd, man/dsyMatrix-class.Rd, tests/Simple.R:
64              bdiag() improvements of last week
65    
66    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
67    
68            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
69              messages
70    
71    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
74            symmetric- or nsparse-Matrix, also fixing the bug introduced with
75            the new version (.999375-10).
76    
77            * tests/Simple.R: regression test for the bugs.
78    
79    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/sparseVector.R (spV2M): fix for "isparseVector".
82            Further, fix <diag> -> <sparseVector> coercion
83            (repSpV): add rep(<sparseVector>, .) method
84    
85            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
86            use as.vector(.).
87    
88            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
89    
90            * R/AllClass.R: new (hidden) class union "scarceMatrix"
91            * R/AllClass.R: sparseVector: add prototype
92    
93            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
94            Kasper Kristensen
95    
96    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * tests/other-pkgs.R: add more interesting Matrix -> graph
99    
100    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
103            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
104    
105    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * DESCRIPTION: release 0.999375-10 to CRAN
108    
109            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
110            .bdiag().
111            * man/bdiag.Rd: update, including test.
112    
113    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * tests/Simple.R: add minimal bdiag() checks
116    
117            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
118              factor out the Tsparse - internal computation into new .bdiag()
119    
120    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * R/nsparseMatrix.R: specific fast all() and any() methods.
123    
124            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
125            when trying to produce too large result.
126    
127            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
128            very large matrices.
129    
130            * R/sparseMatrix.R (printSpMatrix2): new function, used by
131            show(<sparseMatrix>).
132    
133            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
134    
135    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * src/Mutils.c (m_encodeInd, m_encodeInd2):
138            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
139    
140            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
141            big matrices): -> 2nd argument 'di' instead of 'nr' !
142    
143    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/dtCMatrix.R: faster dgC* -> dtC* method
146            * tests/Simple.R: (hence removed "FIXME")
147    
148            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
149            which can be be turned off for possible speed gains.
150    
151    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
154    
155            * R/not.R: fix !<ldiMatrix>
156            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
157    
158            * R/diagMatrix.R (Ops): fix one-off thinko in
159            <diagonal> o <numeric> methods
160    
161            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
162    
163    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
166            * tests/Simple.R: testing the above
167    
168    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
171    
172    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
175            * NAMESPACE (unname): finally exported
176    
177    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/Auxiliaries.R (cholMat): possibly keep packed
180    
181            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
182            for R < 2.7.0.
183    
184            * R/Tsparse.R ([): for triangularMatrix, check if result may be
185            triangular.
186            * tests/indexing.R: regression test
187    
188    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
191            * R/Ops.R: more methods, for lMatrix/nMatrix
192    
193    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * R/expm.R: new file for all expm() methods; notably new ones for
196            diagonal*, triangular*, symmetric* and also simple "matrix".
197    
198    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
201    
202            * inst/test-tools.R (assert.EQ.mat): better message when not equal
203    
204            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
205    
206            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
207            [dl]denseMatrix {identical slots; but more logical method dispatch}
208    
209    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
212    
213            * R/diagMatrix.R (determinant): method
214    
215    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
218    
219            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
220    
221            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
222            its diagonal
223    
224    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
227    
228            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
229    
230            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
231    
232            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
233    
234    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
237    
238            * R/Ops.R (.do.Logic.lsparse): fix NA case
239    
240            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
241    
242            * R/Auxiliaries.R (nnzero): fix special cases, using
243            * R/Auxiliaries.R (indDiag): new utility
244            * R/Auxiliaries.R (indTri): new argument 'diag'
245    
246            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
247    
248    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
251    
252            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
253            ".tCMatrix" triangular matrix.
254    
255            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
256            'clx' can be class *or* class representation.
257            (nnzSparse): new.
258            (non0ind): new 'xtendSymm' argument; used in
259            * R/Ops.R:
260    
261            * R/pMatrix.R: more efficient determinant() method
262    
263    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
266            * [disactivated] NAMESPACE: export(det)
267    
268            * R/diagMatrix.R (mkDiag): new substitute for diag()
269    
270            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
271            (as0, as1): new utility.
272    
273            * R/Csparse.R (diag, band): need diagU2N()
274    
275            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
276    
277            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
278    
279            * R/Ops.R (Compare): fix <nsp> o <nsp> case
280    
281            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
282    
283    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/Auxiliaries.R (signPerm): new utility for
286            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
287    
288            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
289            since we have our own error handler (and can use tryCatch() from R).
290    
291    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
294    
295            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
296            when not positive definite.
297    
298            * R/Auxiliaries.R (asTri): new auxiliary
299            (non0.i): make *much* faster for Tsparse with many non-zero
300            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
301    
302            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
303            test-tools.R , see below
304    
305            * R/dMatrix.R: fix "Summary" method: + diagU2N()
306    
307            * NAMESPACE, R/Matrix.R: add mean() method
308    
309    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
312            cold-hot colors; try *changed* default useAbs = FALSE
313            * man/image-methods.Rd:  nice examples
314    
315    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * inst/test-tools.R (checkMatrix): new function for modularizing part
318            of tstMatrixClass() in tests/Class+Meth.R
319    
320            * R/dsCMatrix.R: coercion from "matrix"
321            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
322    
323            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
324            add test for as(matrix(,0,0), <class>)
325    
326    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
329            work as determinant(matrix(,0,0)).
330    
331            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
332            * man/sparseLU-class.Rd: ditto
333    
334            * R/dgCMatrix.R (determinant): method building on lu()
335            * R/sparseMatrix.R, Matrix.R, ...: ditto
336    
337            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
338    
339    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
342            pattern matrices.
343    
344    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * src/dense.c (dense_to_Csparse): all declarations *before*
347            R_CheckStack(); needed e.g. for ancient gcc 2.96.
348    
349    
350    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * DESCRIPTION (Version): 0.999375-9 --- need to release
353            for R-devel (and R 2.7.0 alpha soon).
354    
355            * R/AllClass.R: drop "double" from "atomicVector" class union
356    
357            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
358            * R/dgeMatrix.R: ditto
359    
360            * R/sparseMatrix.R (summary): count NAs
361    
362            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
363    
364    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
367            order to become compatible to new R 2.7.0 base::rcond().
368    
369    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
372    
373            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
374    
375            * inst/test-tools.R (isValid): new utility, used much in
376            * tests/simple.R:
377    
378            * man/BunchKaufman-methods.Rd: added too
379    
380    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/dsyMatrix.R: add BunchKaufman() methods.
383            * R/dspMatrix.R:
384    
385            * src/init.c: add dsyMatrix_trf
386    
387    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
388    
389            * DESCRIPTION (Version): release 0.999375-7
390            * src/CHMfactor.c (CHMfactor_update): fix
391    
392    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
395            internal_chm_factor().
396    
397            * R/AllGeneric.R: do *not* define a "chol" generic
398                    (but rather use the implicit one *without* making pivot
399                    part of the signature)
400            * R/*.R: drop the 'pivot' from chol's signature and make
401                    'pivot=FALSE' a default argument of method definitions.
402    
403            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
404            version of Matrix
405    
406    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
409    
410            * R/sparseMatrix.R (is.na): new simple method
411            * R/denseMatrix.R (is.na): ditto.
412    
413            * R/diagMatrix.R (.symDiagonal): newly exported utility.
414    
415            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
416    
417            * src/UFsparse_download.sh: -->
418            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
419    
420    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
423            functionality; barely tested in
424            * tests/factorizing.R
425    
426            * src/Csparse.c (diag_tC): new functionality to enable faster
427            determinant(<dsCMatrix>, .) in
428            * R/dsCMatrix.R
429    
430    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
431    
432            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
433              src/CHMfactor.c, src/CHMfactor.h,
434              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
435              Log-determinant of the parent matrix from a CHMfactor object as
436              chm_factor_ldetL2; documentation and support
437    
438    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
439    
440            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
441    
442    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
445            warning.
446    
447    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
450    
451            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
452              <diagonal> o <sparse_triangular>
453              setAs(., "nMatrix") added.
454    
455            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
456    
457            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
458                    new argument 'checkDense = FALSE'.
459    
460    
461    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
464            back-permutation of the matrix exponential.
465    
466            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
467    
468            * DESCRIPTION (Date,Version): ready to release 0.999375-5
469    
470            * tests/simple.R: testing diagN2U
471    
472    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * R/Auxiliaries.R (diagN2U): interface to
475    
476            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
477    
478            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
479    
480    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * src/chm_common.c (chm_diagN2U): new utility.
483    
484            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
485            make use of chm_diagN2U() and hence now preserve triangularity and
486            unit-triangularity.
487    
488            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
489    
490    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
493    
494            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
495            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
496    
497            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
498    
499            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
500    
501            * src/chm_common.c (AS_CHM_FINISH): add note about problem
502            for triangular (diag = "U").
503    
504    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
507            * R/bind.R:  .Call(dense_to_Csparse, *)
508    
509    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
510    
511            * R/Matrix.R (Matrix): no longer use coercions to specific classes
512                    (since we are discouraging them in user code).
513    
514            * tests/*.R: also replaces coercions to specific classes by
515            coercions to super classes.
516    
517            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
518    
519    
520    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
523    
524            * src/dense.c (dense_band): generalized from ddense_band
525    
526            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
527              now for "denseMatrix" (instead of just "ddense*"); much
528              simplified setMethod()s for these.
529    
530            * src/dense.c (dense_to_symmetric): generalized from ddense_*
531    
532    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
535            version of as(*, "symmetricMatric").
536    
537            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
538            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
539    
540    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
541    
542            * R/Matrix.R (subset.ij): utility, as first step to faster
543               M [ <ij-matrix> ] indexing.
544    
545            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
546    
547            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
548            for more efficient symmpart() and skewpart() methods.
549    
550            * src/Mutils.c (equal_string_vectors): utility
551    
552            * src/dense.c (ddense_to_symmetric): new function used in
553    
554            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
555    
556            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
557            order to match the generic (and evade .local(..)).
558    
559            * R/dsCMatrix.R: dgC -> dsC: use C code!
560    
561            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
562            as per TODO
563    
564            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
565    
566            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
567    
568    
569    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
572    
573            * R/Auxiliaries.R (non0.i): take out of non0ind
574    
575            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
576            make tril(), triu(), band() work for "matrix" and all "dense*"
577    
578            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
579            * tests/simple.R: test the fix above
580    
581            * R/sparseMatrix.R ([): simplification: no coerce to <general>
582                    before we use as(., <Tsparse>)[...] anyway
583    
584            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
585    
586            * R/triangularMatrix.R (isTriangular): methods for all subclasses
587            instead of "triangularMatrix" -- just to disambiguate
588    
589    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
592            * tests/indexing.R: example that fails above
593    
594    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
597            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
598                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
599    
600            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
601            * src/Tsparse.h, init.c: ditto
602            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
603                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
604            * R/sparseMatrix.R (isTriangular): hence simplified
605    
606    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * R/Ops.R (.Arith.Csparse): new utility factored out of former
609              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
610    
611    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
612    
613            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
614    
615            * inst/test-tools.R (isOrthogonal): new function; also file restructured
616    
617    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
618    
619            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
620            coercion to "nMatrix" and "pMatrix"
621    
622            * R/AllClass.R: "Schur" class;  "number" class union
623            * man/number-class.Rd:
624            * man/Schur-class.Rd:
625    
626            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
627            (.simpleSchur): Schur() method for diagonal matrices
628            (.triSchur):    Schur() method for triangular matrices
629            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
630    
631    
632    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
635    
636    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
639                    in order to ensure 'system = *' is not lost;
640                    formals()$system instead of cut&paste.
641            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
642    
643    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * DESCRIPTION (Date): make ready for release --> 0.999375-4
646    
647            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
648    
649    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
650    
651            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
652                    and hence does as.vector(.).
653            * man/pMatrix-class.Rd: docs
654            * R/sparseMatrix.R: fix for printing "integer sparse"
655    
656            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
657    
658            * R/Matrix.R and others: use "exact" function argument list for
659                    both "["   : (x, i,j, ..., drop)
660                    and  "[<-" : (x, i,j, ..., value)
661    
662            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
663            * R/Tsparse.R (replTmat):    ditto
664            * R/diagMatrix.R (replDiag): ditto
665            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
666            * tests/indexing.R: testing the above
667    
668    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
669    
670            * R/sparseMatrix.R (cov2cor): method for sparse matrices
671    
672            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
673    
674            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
675    
676            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
677    
678    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * R/Matrix.R: "generic" cov2cor() method
681    
682            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
683                    speed up Q %*% D %*% t(Q)
684            * tests/dpoMatrix.R: test nearPD()
685    
686    2007-12-05  Doug Bates and Martin Maechler
687    
688            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
689            stats::xtabs() allowing to create sparse matrices.
690    
691    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
694    
695    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
698    
699    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
700    
701            * R/LU.R: solve() method for "denseLU"
702    
703    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * DESCRIPTION (Version): 0.999375-3 preparing for release
706    
707            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
708    
709            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
710    
711    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
712    
713            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
714              thanks to Kasper Kristensen.
715            * tests/matprod.R: regression test for that.
716    
717    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
718    
719            * [r4778] R/AllGeneric.R: Check R version before defining generics for
720              primitives
721    
722    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * R/denseMatrix.R (rcond): method
725            * R/sparseQR.R (rcond): method, use x or t(x)
726    
727    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
730            matrices.
731            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
732    
733            * man/rcond.Rd: mention the more general definition, and add
734            example for non-square matrices.
735    
736            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
737    
738    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
739    
740            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
741    
742    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
745            * tests/indexing.R: add new regression for the above cases.
746    
747    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * src/Mutils.h (__sun): clause for alloca.h on Solaris
750    
751    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
752    
753            * DESCRIPTION (Date, Version): 0.999375-2
754    
755    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
756    
757            * R/HBMM.R (readMM): make work for pattern matrices as well
758    
759    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
760    
761            * [r4730] src/Mutils.h: declare alloca
762            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
763              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
764              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
765              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
766              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
767              methods; switch writeMM to use CHOLMOD code; repair readMM
768    
769    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
770    
771            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
772            Oehlschlaegel's ... result type still to be discussed!
773    
774    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
775    
776            * man/image-methods.Rd: new, combining all image() methods
777    
778    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
779    
780            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
781            to work via dgC...
782    
783            * R/Matrix.R (Matrix): special treatment for "table" (S3)
784    
785    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * R/dgTMatrix.R (image): change defaults to
788                    aspect = "iso", colorkey = FALSE
789    
790    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
793            must copy its *expanded* x slot before LAPACK call.
794    
795            * tests/matprod.R: test the last days' changes.
796    
797    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
798    
799            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
800              as well as in sources
801            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
802              Lapack call
803    
804    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
805    
806            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
807                    ("Matrix", "matrix") which is needed in some cases.
808            Ditto for solve().
809    
810            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
811            infinite recursion in dispatch for some cases.
812    
813    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
814    
815            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
816              so pointers match
817    
818    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
819    
820            * DESCRIPTION (Date): set ready for release -- 0.999375-1
821    
822    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
823    
824            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
825              src/chm_common.c, src/chm_common.h: Change API for
826              numeric_as_chm_dense and N_AS_CHM_DN
827    
828    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
829    
830            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
831            * tests/matprod.R: regr.test for it
832    
833    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
834    
835            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
836            * tests/group-methods.R: and regression-test it
837    
838    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
839    
840            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
841              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
842              triplet_to_sparse, documentation, use typedefs
843    
844    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
845    
846            * man/dpoMatrix-class.Rd: added 'corMatrix' example
847    
848            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
849            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
850            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
851    
852            * R/lsparseMatrix.R: bug fix in "all" method
853            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
854    
855            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
856            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
857                    + matrix |-> nMatrix coercion
858            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
859            * man/pMatrix-class.Rd: ditto
860    
861            * R/Matrix.R (Summary): method for non-dMatrix
862    
863            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
864            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
865                    test all Summary methods.
866    
867    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
868    
869            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
870    
871    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
872    
873            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
874    
875            * R/pMatrix.R (t?crossprod): methods for pMatrix
876    
877    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
878    
879            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
880    
881    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
882    
883            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
884              trying to fix a subtle bug - which has been somewhere else.
885    
886    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
887    
888            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
889              solve the bug
890    
891    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
892    
893            * src/dgCMatrix.c (compressed_to_TMatrix):
894    
895    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897            * src/Csparse.c (Rsparse_validate): new, to have some validity
898            checking for RsparseMatrix
899            * src/dgCMatrix.c (xRMatrix_validate): ditto
900            * src/dtCMatrix.c (tRMatrix_validate): ditto
901    
902    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
903    
904            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
905              lgRMatrix
906            * [r4568] DESCRIPTION: Prepare for bug-fix release
907            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
908              for declaration of cholmod_symmetry
909    
910    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
911    
912            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
913            release.
914    
915    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
916    
917            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
918              functions - no longer used
919            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
920              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
921              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
922              Alloca
923    
924    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
925    
926            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
927              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
928              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
929              src/t_gCMatrix_colSums.c: more R_CheckStack()s
930    
931    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
932    
933            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
934              the required amount of memory then call M_numeric_as_chm_dense.
935            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
936              (like Calloc but calling alloca)
937    
938    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
939    
940            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
941            and extended with more sophisticated 'col.names' option.
942            * NAMESPACE: export  printSparseMatrix()
943            * man/printSpMatrix.Rd: document, incl. examples
944    
945    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
946    
947            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
948              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
949              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
950    
951    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
952    
953            * DESCRIPTION (Version): 0.99875-4
954    
955            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
956            some dimnames perservation.
957    
958            * R/dsTMatrix.R (t-method): keep dimnames
959            * R/dtTMatrix.R:  ditto
960    
961            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
962            and ncol(.) < 10
963    
964            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
965            from Mutils.h
966    
967            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
968            e.g. in as(<ngCMatrix>, "matrix")
969    
970    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
971    
972            * [r4529] .: Create a branch for the API changes from the 0.99875
973              series to the 0.999375 series
974            * [r4530] DESCRIPTION, inst/include/Matrix.h,
975              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
976              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
977              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
978              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
979              as_cholmod_x functions
980    
981    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
982    
983            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
984              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
985              to Comparisons
986    
987    >>>>>>> .merge-right.r4561
988    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
989    
990            * DESCRIPTION (Version): 0.99875-3 ready to be released.
991    
992            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
993    
994            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
995            that should also work in a future version of R.
996    
997  2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
998    
999          * NAMESPACE, R/AllClass.R: "xsparseVector" class union.          * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
# Line 5  Line 1001 
1001          * R/sparseVector.R: more *sparseVector coercions, notably for          * R/sparseVector.R: more *sparseVector coercions, notably for
1002          non - double ones.          non - double ones.
1003    
   
1004  2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1005    
1006          * R/colSums.R: new file for all (col|row)(Sums|Means) methods,          * R/colSums.R: new file for all (col|row)(Sums|Means) methods,

Legend:
Removed from v.1922  
changed lines
  Added in v.2227

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge