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revision 1847, Sat May 19 19:23:28 2007 UTC revision 2206, Wed Jun 25 14:57:02 2008 UTC
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1    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
4            .bdiag().
5            * man/bdiag.Rd: update, including test.
6    
7    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * tests/Simple.R: add minimal bdiag() checks
10    
11            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
12              factor out the Tsparse - internal computation into new .bdiag()
13    
14    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * R/nsparseMatrix.R: specific fast all() and any() methods.
17    
18            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
19            when trying to produce too large result.
20    
21            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
22            very large matrices.
23    
24            * R/sparseMatrix.R (printSpMatrix2): new function, used by
25            show(<sparseMatrix>).
26    
27            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
28    
29    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * src/Mutils.c (m_encodeInd, m_encodeInd2):
32            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
33    
34            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
35            big matrices): -> 2nd argument 'di' instead of 'nr' !
36    
37    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/dtCMatrix.R: faster dgC* -> dtC* method
40            * tests/Simple.R: (hence removed "FIXME")
41    
42            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
43            which can be be turned off for possible speed gains.
44    
45    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
48    
49            * R/not.R: fix !<ldiMatrix>
50            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
51    
52            * R/diagMatrix.R (Ops): fix one-off thinko in
53            <diagonal> o <numeric> methods
54    
55            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
56    
57    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
60            * tests/Simple.R: testing the above
61    
62    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
65    
66    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
69            * NAMESPACE (unname): finally exported
70    
71    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/Auxiliaries.R (cholMat): possibly keep packed
74    
75            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
76            for R < 2.7.0.
77    
78            * R/Tsparse.R ([): for triangularMatrix, check if result may be
79            triangular.
80            * tests/indexing.R: regression test
81    
82    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
85            * R/Ops.R: more methods, for lMatrix/nMatrix
86    
87    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/expm.R: new file for all expm() methods; notably new ones for
90            diagonal*, triangular*, symmetric* and also simple "matrix".
91    
92    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
95    
96            * inst/test-tools.R (assert.EQ.mat): better message when not equal
97    
98            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
99    
100            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
101            [dl]denseMatrix {identical slots; but more logical method dispatch}
102    
103    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
106    
107            * R/diagMatrix.R (determinant): method
108    
109    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
112    
113            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
114    
115            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
116            its diagonal
117    
118    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
121    
122            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
123    
124            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
125    
126            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
127    
128    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
131    
132            * R/Ops.R (.do.Logic.lsparse): fix NA case
133    
134            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
135    
136            * R/Auxiliaries.R (nnzero): fix special cases, using
137            * R/Auxiliaries.R (indDiag): new utility
138            * R/Auxiliaries.R (indTri): new argument 'diag'
139    
140            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
141    
142    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
145    
146            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
147            ".tCMatrix" triangular matrix.
148    
149            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
150            'clx' can be class *or* class representation.
151            (nnzSparse): new.
152            (non0ind): new 'xtendSymm' argument; used in
153            * R/Ops.R:
154    
155            * R/pMatrix.R: more efficient determinant() method
156    
157    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
160            * [disactivated] NAMESPACE: export(det)
161    
162            * R/diagMatrix.R (mkDiag): new substitute for diag()
163    
164            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
165            (as0, as1): new utility.
166    
167            * R/Csparse.R (diag, band): need diagU2N()
168    
169            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
170    
171            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
172    
173            * R/Ops.R (Compare): fix <nsp> o <nsp> case
174    
175            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
176    
177    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/Auxiliaries.R (signPerm): new utility for
180            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
181    
182            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
183            since we have our own error handler (and can use tryCatch() from R).
184    
185    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
188    
189            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
190            when not positive definite.
191    
192            * R/Auxiliaries.R (asTri): new auxiliary
193            (non0.i): make *much* faster for Tsparse with many non-zero
194            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
195    
196            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
197            test-tools.R , see below
198    
199            * R/dMatrix.R: fix "Summary" method: + diagU2N()
200    
201            * NAMESPACE, R/Matrix.R: add mean() method
202    
203    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
206            cold-hot colors; try *changed* default useAbs = FALSE
207            * man/image-methods.Rd:  nice examples
208    
209    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * inst/test-tools.R (checkMatrix): new function for modularizing part
212            of tstMatrixClass() in tests/Class+Meth.R
213    
214            * R/dsCMatrix.R: coercion from "matrix"
215            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
216    
217            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
218            add test for as(matrix(,0,0), <class>)
219    
220    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
223            work as determinant(matrix(,0,0)).
224    
225            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
226            * man/sparseLU-class.Rd: ditto
227    
228            * R/dgCMatrix.R (determinant): method building on lu()
229            * R/sparseMatrix.R, Matrix.R, ...: ditto
230    
231            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
232    
233    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
236            pattern matrices.
237    
238    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * src/dense.c (dense_to_Csparse): all declarations *before*
241            R_CheckStack(); needed e.g. for ancient gcc 2.96.
242    
243    
244    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * DESCRIPTION (Version): 0.999375-9 --- need to release
247            for R-devel (and R 2.7.0 alpha soon).
248    
249            * R/AllClass.R: drop "double" from "atomicVector" class union
250    
251            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
252            * R/dgeMatrix.R: ditto
253    
254            * R/sparseMatrix.R (summary): count NAs
255    
256            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
257    
258    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
261            order to become compatible to new R 2.7.0 base::rcond().
262    
263    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
266    
267            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
268    
269            * inst/test-tools.R (isValid): new utility, used much in
270            * tests/simple.R:
271    
272            * man/BunchKaufman-methods.Rd: added too
273    
274    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/dsyMatrix.R: add BunchKaufman() methods.
277            * R/dspMatrix.R:
278    
279            * src/init.c: add dsyMatrix_trf
280    
281    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
282    
283            * DESCRIPTION (Version): release 0.999375-7
284            * src/CHMfactor.c (CHMfactor_update): fix
285    
286    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
289            internal_chm_factor().
290    
291            * R/AllGeneric.R: do *not* define a "chol" generic
292                    (but rather use the implicit one *without* making pivot
293                    part of the signature)
294            * R/*.R: drop the 'pivot' from chol's signature and make
295                    'pivot=FALSE' a default argument of method definitions.
296    
297            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
298            version of Matrix
299    
300    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
303    
304            * R/sparseMatrix.R (is.na): new simple method
305            * R/denseMatrix.R (is.na): ditto.
306    
307            * R/diagMatrix.R (.symDiagonal): newly exported utility.
308    
309            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
310    
311            * src/UFsparse_download.sh: -->
312            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
313    
314    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
317            functionality; barely tested in
318            * tests/factorizing.R
319    
320            * src/Csparse.c (diag_tC): new functionality to enable faster
321            determinant(<dsCMatrix>, .) in
322            * R/dsCMatrix.R
323    
324    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
325    
326            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
327              src/CHMfactor.c, src/CHMfactor.h,
328              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
329              Log-determinant of the parent matrix from a CHMfactor object as
330              chm_factor_ldetL2; documentation and support
331    
332    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
335    
336    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
339            warning.
340    
341    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
344    
345            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
346              <diagonal> o <sparse_triangular>
347              setAs(., "nMatrix") added.
348    
349            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
350    
351            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
352                    new argument 'checkDense = FALSE'.
353    
354    
355    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
358            back-permutation of the matrix exponential.
359    
360            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
361    
362            * DESCRIPTION (Date,Version): ready to release 0.999375-5
363    
364            * tests/simple.R: testing diagN2U
365    
366    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/Auxiliaries.R (diagN2U): interface to
369    
370            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
371    
372            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
373    
374    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * src/chm_common.c (chm_diagN2U): new utility.
377    
378            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
379            make use of chm_diagN2U() and hence now preserve triangularity and
380            unit-triangularity.
381    
382            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
383    
384    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
387    
388            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
389            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
390    
391            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
392    
393            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
394    
395            * src/chm_common.c (AS_CHM_FINISH): add note about problem
396            for triangular (diag = "U").
397    
398    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
401            * R/bind.R:  .Call(dense_to_Csparse, *)
402    
403    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * R/Matrix.R (Matrix): no longer use coercions to specific classes
406                    (since we are discouraging them in user code).
407    
408            * tests/*.R: also replaces coercions to specific classes by
409            coercions to super classes.
410    
411            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
412    
413    
414    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
417    
418            * src/dense.c (dense_band): generalized from ddense_band
419    
420            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
421              now for "denseMatrix" (instead of just "ddense*"); much
422              simplified setMethod()s for these.
423    
424            * src/dense.c (dense_to_symmetric): generalized from ddense_*
425    
426    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
429            version of as(*, "symmetricMatric").
430    
431            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
432            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
433    
434    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * R/Matrix.R (subset.ij): utility, as first step to faster
437               M [ <ij-matrix> ] indexing.
438    
439            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
440    
441            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
442            for more efficient symmpart() and skewpart() methods.
443    
444            * src/Mutils.c (equal_string_vectors): utility
445    
446            * src/dense.c (ddense_to_symmetric): new function used in
447    
448            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
449    
450            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
451            order to match the generic (and evade .local(..)).
452    
453            * R/dsCMatrix.R: dgC -> dsC: use C code!
454    
455            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
456            as per TODO
457    
458            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
459    
460            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
461    
462    
463    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
464    
465            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
466    
467            * R/Auxiliaries.R (non0.i): take out of non0ind
468    
469            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
470            make tril(), triu(), band() work for "matrix" and all "dense*"
471    
472            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
473            * tests/simple.R: test the fix above
474    
475            * R/sparseMatrix.R ([): simplification: no coerce to <general>
476                    before we use as(., <Tsparse>)[...] anyway
477    
478            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
479    
480            * R/triangularMatrix.R (isTriangular): methods for all subclasses
481            instead of "triangularMatrix" -- just to disambiguate
482    
483    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
484    
485            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
486            * tests/indexing.R: example that fails above
487    
488    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
489    
490            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
491            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
492                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
493    
494            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
495            * src/Tsparse.h, init.c: ditto
496            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
497                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
498            * R/sparseMatrix.R (isTriangular): hence simplified
499    
500    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * R/Ops.R (.Arith.Csparse): new utility factored out of former
503              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
504    
505    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
508    
509            * inst/test-tools.R (isOrthogonal): new function; also file restructured
510    
511    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
514            coercion to "nMatrix" and "pMatrix"
515    
516            * R/AllClass.R: "Schur" class;  "number" class union
517            * man/number-class.Rd:
518            * man/Schur-class.Rd:
519    
520            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
521            (.simpleSchur): Schur() method for diagonal matrices
522            (.triSchur):    Schur() method for triangular matrices
523            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
524    
525    
526    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
527    
528            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
529    
530    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
531    
532            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
533                    in order to ensure 'system = *' is not lost;
534                    formals()$system instead of cut&paste.
535            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
536    
537    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * DESCRIPTION (Date): make ready for release --> 0.999375-4
540    
541            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
542    
543    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
546                    and hence does as.vector(.).
547            * man/pMatrix-class.Rd: docs
548            * R/sparseMatrix.R: fix for printing "integer sparse"
549    
550            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
551    
552            * R/Matrix.R and others: use "exact" function argument list for
553                    both "["   : (x, i,j, ..., drop)
554                    and  "[<-" : (x, i,j, ..., value)
555    
556            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
557            * R/Tsparse.R (replTmat):    ditto
558            * R/diagMatrix.R (replDiag): ditto
559            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
560            * tests/indexing.R: testing the above
561    
562    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * R/sparseMatrix.R (cov2cor): method for sparse matrices
565    
566            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
567    
568            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
569    
570            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
571    
572    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * R/Matrix.R: "generic" cov2cor() method
575    
576            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
577                    speed up Q %*% D %*% t(Q)
578            * tests/dpoMatrix.R: test nearPD()
579    
580    2007-12-05  Doug Bates and Martin Maechler
581    
582            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
583            stats::xtabs() allowing to create sparse matrices.
584    
585    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
588    
589    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
592    
593    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * R/LU.R: solve() method for "denseLU"
596    
597    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * DESCRIPTION (Version): 0.999375-3 preparing for release
600    
601            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
602    
603            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
604    
605    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
608              thanks to Kasper Kristensen.
609            * tests/matprod.R: regression test for that.
610    
611    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
612    
613            * [r4778] R/AllGeneric.R: Check R version before defining generics for
614              primitives
615    
616    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
617    
618            * R/denseMatrix.R (rcond): method
619            * R/sparseQR.R (rcond): method, use x or t(x)
620    
621    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
622    
623            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
624            matrices.
625            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
626    
627            * man/rcond.Rd: mention the more general definition, and add
628            example for non-square matrices.
629    
630            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
631    
632    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
635    
636    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
639            * tests/indexing.R: add new regression for the above cases.
640    
641    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * src/Mutils.h (__sun): clause for alloca.h on Solaris
644    
645    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
646    
647            * DESCRIPTION (Date, Version): 0.999375-2
648    
649    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
650    
651            * R/HBMM.R (readMM): make work for pattern matrices as well
652    
653    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
654    
655            * [r4730] src/Mutils.h: declare alloca
656            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
657              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
658              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
659              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
660              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
661              methods; switch writeMM to use CHOLMOD code; repair readMM
662    
663    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
666            Oehlschlaegel's ... result type still to be discussed!
667    
668    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
669    
670            * man/image-methods.Rd: new, combining all image() methods
671    
672    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
675            to work via dgC...
676    
677            * R/Matrix.R (Matrix): special treatment for "table" (S3)
678    
679    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
680    
681            * R/dgTMatrix.R (image): change defaults to
682                    aspect = "iso", colorkey = FALSE
683    
684    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
687            must copy its *expanded* x slot before LAPACK call.
688    
689            * tests/matprod.R: test the last days' changes.
690    
691    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
692    
693            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
694              as well as in sources
695            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
696              Lapack call
697    
698    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
701                    ("Matrix", "matrix") which is needed in some cases.
702            Ditto for solve().
703    
704            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
705            infinite recursion in dispatch for some cases.
706    
707    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
708    
709            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
710              so pointers match
711    
712    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
713    
714            * DESCRIPTION (Date): set ready for release -- 0.999375-1
715    
716    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
717    
718            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
719              src/chm_common.c, src/chm_common.h: Change API for
720              numeric_as_chm_dense and N_AS_CHM_DN
721    
722    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
725            * tests/matprod.R: regr.test for it
726    
727    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
730            * tests/group-methods.R: and regression-test it
731    
732    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
733    
734            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
735              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
736              triplet_to_sparse, documentation, use typedefs
737    
738    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
739    
740            * man/dpoMatrix-class.Rd: added 'corMatrix' example
741    
742            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
743            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
744            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
745    
746            * R/lsparseMatrix.R: bug fix in "all" method
747            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
748    
749            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
750            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
751                    + matrix |-> nMatrix coercion
752            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
753            * man/pMatrix-class.Rd: ditto
754    
755            * R/Matrix.R (Summary): method for non-dMatrix
756    
757            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
758            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
759                    test all Summary methods.
760    
761    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
764    
765    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
768    
769            * R/pMatrix.R (t?crossprod): methods for pMatrix
770    
771    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
772    
773            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
774    
775    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
776    
777            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
778              trying to fix a subtle bug - which has been somewhere else.
779    
780    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
781    
782            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
783              solve the bug
784    
785    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * src/dgCMatrix.c (compressed_to_TMatrix):
788    
789    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * src/Csparse.c (Rsparse_validate): new, to have some validity
792            checking for RsparseMatrix
793            * src/dgCMatrix.c (xRMatrix_validate): ditto
794            * src/dtCMatrix.c (tRMatrix_validate): ditto
795    
796    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
797    
798            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
799              lgRMatrix
800            * [r4568] DESCRIPTION: Prepare for bug-fix release
801            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
802              for declaration of cholmod_symmetry
803    
804    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
805    
806            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
807            release.
808    
809    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
810    
811            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
812              functions - no longer used
813            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
814              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
815              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
816              Alloca
817    
818    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
819    
820            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
821              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
822              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
823              src/t_gCMatrix_colSums.c: more R_CheckStack()s
824    
825    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
826    
827            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
828              the required amount of memory then call M_numeric_as_chm_dense.
829            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
830              (like Calloc but calling alloca)
831    
832    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
833    
834            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
835            and extended with more sophisticated 'col.names' option.
836            * NAMESPACE: export  printSparseMatrix()
837            * man/printSpMatrix.Rd: document, incl. examples
838    
839    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
840    
841            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
842              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
843              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
844    
845    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
846    
847            * DESCRIPTION (Version): 0.99875-4
848    
849            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
850            some dimnames perservation.
851    
852            * R/dsTMatrix.R (t-method): keep dimnames
853            * R/dtTMatrix.R:  ditto
854    
855            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
856            and ncol(.) < 10
857    
858            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
859            from Mutils.h
860    
861            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
862            e.g. in as(<ngCMatrix>, "matrix")
863    
864    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
865    
866            * [r4529] .: Create a branch for the API changes from the 0.99875
867              series to the 0.999375 series
868            * [r4530] DESCRIPTION, inst/include/Matrix.h,
869              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
870              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
871              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
872              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
873              as_cholmod_x functions
874    
875    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
876    
877            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
878              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
879              to Comparisons
880    
881    >>>>>>> .merge-right.r4561
882    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
883    
884            * DESCRIPTION (Version): 0.99875-3 ready to be released.
885    
886            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
887    
888            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
889            that should also work in a future version of R.
890    
891    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
892    
893            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
894    
895            * R/sparseVector.R: more *sparseVector coercions, notably for
896            non - double ones.
897    
898    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
899    
900            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
901              notably the new ones building on the new .Call(.)s:
902    
903            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
904            all 4 of [dlin]gCMatrix_colSums().
905    
906    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
907    
908            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
909            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
910              result
911    
912    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
913    
914            * R/kronecker.R: fix typo (could lead to inf.recursion)
915            * test/simple.R: testing that
916    
917            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
918            method as well (which can have arguments, show() can't).
919    
920    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
921    
922            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
923              added dgCMatrix_colSums for [col,row][Sums,Means]
924    
925    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
926    
927            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
928              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
929              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
930            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
931              class
932            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
933              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
934              row names to store the levels - duh!  Added an example.
935    
936    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
937    
938            * src/Csparse.c (Csparse_validate): check for *repeated* entries
939            thanks to example from Christian Buchta; with a test here:
940            * tests/simple.R:
941    
942    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
943    
944            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
945            of colSums(*, sparseResult = TRUE)
946    
947    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
948    
949            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
950            'na.rm = FALSE' as "everywhere" else in R.
951    
952    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
953    
954            * [r4421] src/CSparse_install.sh: Modify for new organization of
955              CSparse package
956            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
957              SuiteSparse
958            * [r4426] src/Makefile: add ./UFconfig to the include path for
959              compilation
960            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
961            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
962              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
963    
964    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
965    
966            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
967            * R/sparseMatrix.R (prSpMatrix): now gives a message about
968            suppressed column names.
969    
970    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
971    
972            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
973              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
974              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
975              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
976              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
977              Remove warnings after change to const char* CHAR
978    
979    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
980    
981            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
982              type of M_cholmod_ssmult
983    
984    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
985    
986            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
987              src/init.c: Yet another cholmod export - cholmod_ssmult
988    
989    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
990    
991            * NAMESPACE: exported drop0(), since
992            * man/drop0.Rd: I have seen several cases, I really wanted to use
993            it, so our users may want too.
994    
995    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997            * man/colSums.Rd: separately document colSums() etc, since these
998            have the extra argument 'sparseResult'.
999    
1000    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1001    
1002            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
1003            * man/spMatrix.Rd: docu., including examples
1004    
1005            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
1006            in order to make colMeans() etc fast *and* correct.
1007            * R/sparseVector.R (replSPvec): "[<-" functionality for
1008            sparseVectors; tested in
1009            * tests/simple.R:
1010    
1011    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1012    
1013            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1014            (very) sparse Matrices; output similar to Matlab's print().
1015    
1016  2007-05-17  Douglas Bates  <bates@stat.wisc.edu>  2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
1017    
1018          * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not          * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not

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