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revision 1548, Mon Sep 11 22:13:07 2006 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>
1017    
1018            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
1019            0-based, indices (Jose Quesada <quesada@gmail.com>).
1020    
1021    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
1022    
1023            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
1024    
1025    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1026    
1027            * R/Auxiliaries.R (sparsapply): new utility, much faster than
1028            tapply1() for large sparse matrices.
1029    
1030    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1031    
1032            * R/Matrix.R (dim<-): reshape now via sparseVector.
1033    
1034            * R/sparseVector.R: methods and function for
1035            * R/AllClass.R: new "sparseVector" class and daughters.
1036            * NAMESPACE: export new classes
1037    
1038    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1039    
1040            * DESCRIPTION (Version): 0.99875-1
1041            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1042    
1043    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1044    
1045            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1046            indexing
1047            * tests/indexing.R: test set for that.
1048    
1049    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1050    
1051            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1052            entries.
1053            * tests/indexing.R(out): add regression test for it
1054    
1055    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1056    
1057            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1058            name for "!" method definitions.
1059    
1060    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1061    
1062            * R/Tsparse.R (intI): new utility, used for "[" :
1063                    Cleanup up there, and fixes for duplicated indices - more TODO!
1064    
1065            * tests/indexing.R(out): more tests
1066    
1067    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1068    
1069            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1070            code that is now part of the R Lapack library.
1071    
1072            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1073            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1074    
1075    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1076    
1077            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1078    
1079    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1080    
1081            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1082            up with extraneous names '0'...'<n-1>'
1083    
1084    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1085    
1086            * R/dgTMatrix.R (mat2dgT): care about NAs
1087    
1088    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1089    
1090            * R/kronecker.R: triangularity preserving methods
1091    
1092    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1093    
1094            * R/kronecker.R: new file collecting kronecker() methods in one
1095                    place.  Goal: become much faster!
1096    
1097    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1098    
1099            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1100            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1101            can be much faster.
1102    
1103            * tests/matprod.R: add regression tests for these (upper & lower).
1104    
1105    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1106    
1107            * R/Matrix.R (diff): method for our Matrices.
1108    
1109            * R/sparseMatrix.R (isDiagonal): check dim()!
1110    
1111    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1112    
1113            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1114            proposal from Tamas Papp.
1115    
1116    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1117    
1118            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1119    
1120            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1121            rather define and export  cBind() and rBind() only.
1122            --> useRs *must* change code that used to have cbind()/rbind() !!
1123    
1124            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1125            * R/bind.Rout.save: ditto
1126    
1127    2007-02-16  Douglas Bates  <bates@r-project.org>
1128    
1129            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1130            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1131            const modifier on declaration of the array 'valid'
1132    
1133    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1134    
1135            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1136    
1137    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1138    
1139            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1140    
1141            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1142            * tests/simple.R: test the above and some of these coercions:
1143    
1144            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1145                    be careful to avoid infinite recursion, using new coercions in
1146            * R/ngCMatrix.R and nsC... and ntC...
1147            * R/lsparseMatrix.R: ditto
1148    
1149            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1150    
1151            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1152            * R/Rsparse.R: reactivate .Call()s
1153    
1154            * tests/Class+Meth.R: a bit more on actual classes
1155    
1156    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1157    
1158            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1159    
1160    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1161    
1162            * DESCRIPTION (Version): 0.9975-10 to upload
1163    
1164            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1165            specific classes less unconditionally.
1166    
1167            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1168    
1169            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1170    
1171            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1172            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1173            R_to_CMatrix segfaults on one platform.
1174            Eliminate most coercion method to *specific* classes, and replace
1175            with virtual classes coercions.
1176    
1177    
1178    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1179    
1180            * src/init.c: export the CHM...._validate() placeholders, since
1181            they *are* called.
1182    
1183            * tests/Class+Meth.R (classCanCoerce): and starting to test
1184            all as(<from>, <to>)
1185    
1186    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1187    
1188            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1189            * tests/indexing.R: tested now
1190            * tests/indexing.Rout.save: updated
1191    
1192            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1193            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1194            appropriate.
1195    
1196            * NAMESPACE: export a trivial
1197            * R/Matrix.R: drop() Matrix-method
1198    
1199            * R/AllClass.R: moved all prototypes to virtual super classes.
1200    
1201            * R/Rsparse.R: many more coercions to have less exceptions in
1202            * tests/Class+Meth.R:
1203    
1204            * R/Ops.R (Compare): tweak for case with NA
1205            * tests/simpl.R: hence another 'FIXME' eliminated
1206    
1207    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1208    
1209            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1210            objects.
1211    
1212            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1213              and more of "!", "&", "|", all, any; coercions
1214    
1215            * R/Rsparse.R: many coercions (which enable quite a few other
1216            methods), thanks to enhancements in
1217            * src/dgCMatrix.c (R_to_CMatrix): new, and
1218            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1219            symmetric & triangular and ..RMatrix objects.
1220    
1221            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1222            renamed file from src/dsTMatrix.c;
1223            now dealing with symmetric and triangular Tsparse coercions, both
1224            to dense and general.
1225    
1226    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1227    
1228            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1229    
1230            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1231            where sensible when the <numeric> is of length > 1.
1232    
1233    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1234    
1235            * R/Matrix.R ([<-): for M[] <- value: fix length
1236    
1237    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1238    
1239            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1240            * R/ndenseMatrix.R: new coercions n* -> l*
1241    
1242    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1243    
1244            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1245    
1246            * R/Ops.R ("Logic"): and other "Ops", many updates
1247    
1248    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1249    
1250            * src/Mutils.h (SET_DimNames): new utility
1251    
1252            * R/Auxiliaries.R (nnzero): improved and now exported via
1253    
1254            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1255    
1256    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1257    
1258            * R/diagMatrix.R (!): fix typo.
1259    
1260    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1261    
1262            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1263                    allow to pass class definition --> speedup
1264            * R/sparseMatrix.R: apply the above
1265    
1266            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1267    
1268            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1269            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1270            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1271    
1272            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1273    
1274            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1275            and use it for "sparse*" as well, since it's faster than the
1276            as_Csparse(.) way.
1277    
1278    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1279    
1280            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1281    
1282    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1283    
1284            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1285            as method for   M[ ij ] <- v
1286            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1287    
1288            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1289            FALSE answer
1290    
1291            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1292            * tests/indexing.R: test it, and some of the above
1293    
1294    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1295    
1296            * R/Auxiliaries.R (is_duplicatedT): new utility
1297    
1298    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1299    
1300            * src/init.c (R_init_Matrix): export cholmod_scale
1301    
1302    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1303    
1304            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1305            base::as.matrix to (x, ...)
1306    
1307    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1308    
1309            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1310            file; start using "Logic", hence
1311    
1312            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1313            * NAMESPACE: import and export "Logic"
1314    
1315    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1316    
1317            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1318            only needed previously to R version 2.5.0.
1319    
1320    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1321    
1322            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1323    
1324            * R/Tsparse.R (replTmat): fix subassignment of triangular
1325            * R/Csparse.R (replCmat): ditto
1326            * tests/indexing.R: more tests, incl the above fix
1327    
1328    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1329    
1330            * R/Auxiliaries.R (drop0): extend for non CSparse
1331            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1332    
1333            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1334                    use uplo correctly (!); other places: use uplo_P() macro
1335    
1336            * R/Csparse.R (replCmat): call diagU2N() when needed
1337            * R/Tsparse.R (replTmat): ditto
1338    
1339            * src/dtCMatrix.c (tCMatrix_validate): new
1340            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1341            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1342    
1343            * R/diagMatrix.R (replDiag): to use in [<-
1344    
1345    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1346    
1347            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1348                    also more general diagU2N().
1349    
1350    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1351    
1352            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1353            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1354    
1355    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1356    
1357            * tests/bind.R: a few more cases
1358            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1359    
1360            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1361            * R/ddenseMatrix.R (cbind2/rbind2)
1362            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1363            * tests/indexing.R
1364            * tests/indexing.Rout.save: updated
1365    
1366    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1367    
1368            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1369            * tests/indexing.R
1370    
1371    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1372    
1373            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1374            align with proper position of "0", i.e., right for integers.
1375            argument 'align' by default is "fancy".
1376    
1377    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1378    
1379            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1380            * R/Csparse.R: and fix "Compare" for more cases.
1381            * tests/Class+Meth.R: test some of these (m == m, m != m)
1382    
1383    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1384    
1385            * R/lsparseMatrix.R: all() and any() methods
1386            * R/ldenseMatrix.R:      ditto
1387            * NAMESPACE, R/Matrix.R: ditto
1388    
1389            * man/all-methods.Rd: document them minimally
1390    
1391            * tests/simple.R: add a few examples for these
1392    
1393    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1394    
1395            * R/Tsparse.R ([): fix long standing typo in symmetric case
1396            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1397    
1398    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1399    
1400            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1401            to LL before converting to a sparse matrix. (The LDL form can be
1402            converted to a sparse matrix but it is implicitly a unit
1403            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1404    
1405    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1406    
1407            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1408    
1409    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1410    
1411            * DESCRIPTION (Version): updated -> release 0.9975-7
1412            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1413    
1414    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1415    
1416            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1417    
1418    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1419    
1420            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1421            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1422            is exactly singular.
1423    
1424    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1425    
1426            * DESCRIPTION (Date): updated -> release 0.9975-6
1427    
1428    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1429    
1430            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1431            now returns symmetric.
1432    
1433            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1434    
1435            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1436            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1437    
1438            * R/Auxiliaries.R (.type.kind): added
1439    
1440    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1441    
1442            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1443            running src/CSparse_install.sh
1444    
1445            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1446    
1447    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1448    
1449            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1450            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1451    
1452            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1453    
1454            * tests/Class+Meth.R (tstMatrixClass): now assure
1455            the (important in method programming) property :
1456    
1457                    ###>>  Every "Matrix" is either
1458                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1459    
1460                    (where "*" stands for "Matrix")
1461    
1462            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1463    
1464            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1465            * tests/validObj.R: checks for "comparison"
1466    
1467            * R/sparseMatrix.R ([): improved indexing for sparse;
1468                    trying to keep <symmetric>[ n, n] symmmetric
1469    
1470            * tests/indexing.R: indexing for logical sparse now ok
1471    
1472    
1473    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1474    
1475            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1476    
1477            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1478    
1479    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1480    
1481            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1482    
1483            * tests/simple.R: validObject() checking the above.
1484    
1485            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1486            replacing both dgCMatrix_validate and lgCM*.
1487    
1488            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1489            fix dimnames setting in other places.
1490            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1491    
1492    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1493    
1494            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1495    
1496            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1497            symmetry test, via
1498            * R/Auxiliaries.R (.as.dgC.0.factors):
1499    
1500    2006-11-01  Douglas Bates  <bates@r-project.org>
1501    
1502            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1503            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1504            <CsparseMatrix>) added
1505    
1506    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1507    
1508            * tests/matprod.R: add a variation of Harri's example
1509    
1510            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1511            recursive infinitely.
1512    
1513            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1514    
1515            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1516    
1517    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1518    
1519            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1520            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1521            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1522            satisfy the above test.
1523    
1524    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1525    
1526            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1527    
1528            * R/dgCMatrix.R: solve(a, b="missing") based on
1529            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1530            RHS = NULL.
1531    
1532            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1533            add more (needed) [t]crossprod() methods.
1534    
1535            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1536    
1537            * R/Auxiliaries.R (as_CspClass): cleanup
1538            (drop0): internal utility for "Csparse_drop(*, 0)"
1539            (.bail.out.2): encourage active feedback
1540    
1541    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1542    
1543            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1544    
1545            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1546            non-valid or 'sorted' case).
1547    
1548            * R/dsparseMatrix.R: add "chol" method.
1549            * R/ddenseMatrix.R: ditto
1550    
1551            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1552            * NAMESPACE (Ops)
1553            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1554            coercion; deprecating direct lower level coercions.
1555    
1556            * R/*.R (seq): use seq_len() and seq_along() where possible.
1557    
1558    
1559    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1560    
1561            * DESCRIPTION (Version): 0.9975-5 ready for release
1562    
1563    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1564    
1565            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1566    
1567    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1568    
1569            * R/AllClass.R (corMatrix): add 'validity' check;
1570                    comment out unused "LDL" class definition
1571            * NAMESPACE: mention, but do not export "LDL" class
1572            * R/corMatrix.R: new (simple), needed for R-devel with
1573            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1574              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1575    
1576    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1577    
1578            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1579            use Rprintf and R's error handling.
1580    
1581    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1582    
1583            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1584            * tests/matprod.R: add tests for the bug fixed.
1585    
1586    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1587    
1588            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1589            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1590    
1591    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1592    
1593            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1594    
1595    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1596    
1597            * DESCRIPTION (Version): 0.9975-3
1598    
1599            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1600            (sparse) matrices.
1601            * man/bdiag.Rd: docu + examples
1602    
1603            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1604    
1605            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1606            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1607    
1608            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1609            that result is sparse or diagonal (and not dense).
1610    
1611            * man/Subassign-methods.Rd: fix examples
1612    
1613            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1614            should always return a sparse (and not sometimes a diagonal) matrix.
1615    
1616    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1617    
1618            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1619    
1620    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1621    
1622            * DESCRIPTION (Version): 0.9975-2
1623    
1624            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1625    
1626    2006-10-02  Douglas Bates  <bates@R-project.org>
1627    
1628            * tests/dg_Matrix.R: Simplify test taking into account new code.
1629    
1630    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1631    
1632            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1633    
1634            * R/lsTMatrix.R: new files w/ missing methods
1635            * R/nsTMatrix.R:  "  'for completeness'
1636    
1637            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1638    
1639            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1640    
1641    
1642    2006-09-28  Douglas Bates  <bates@R-project.org>
1643    
1644            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1645            included.
1646    
1647            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1648            Export C-callable functions used in Zt_create in lme4.
1649    
1650    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1651    
1652            * DESCRIPTION (Version): 0.9975-1
1653    
1654            * tests/simple.R: less checks fail; using NA, found that our
1655                    kronecker() is not base-compatible with NA's.
1656    
1657            * R/dMatrix.R: "Compare" method now implemented for all cases
1658    
1659            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1660    
1661            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1662    
1663            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1664            * src/dspMatrix.c (dspMatrix_validate): ditto
1665    
1666            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1667              including coercion to [nl]tTMatrix.
1668    
1669            * R/diagMatrix.R (show): print a header line as for other classes.
1670    
1671    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1672    
1673            * src/Makefile.win (SUBDIRS): fix typo
1674    
1675    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1676    
1677            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1678    
1679    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1680    
1681            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1682            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1683            accept a symmetric matrix).
1684            * tests/group-methods.R: Uncomment test of crossprod applied to
1685            lsCMatrix objects.
1686    
1687    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1688    
1689            * R/AllClass.R (symmetricMatrix): add validity method (available
1690            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1691    
1692            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1693    
1694            * tests/indexing.Rout.save:
1695            * tests/indexing.R: additions, mainly for 'lsparse'
1696    
1697            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1698            case.
1699    
1700            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1701    
1702    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1703    
1704            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1705                    as 'N' (1-letter - Ok?)
1706    
1707            * tests/group-methods.R: add test for logical + NAs
1708    
1709            * R/dMatrix.R ("Compare"): fix to work with NA's
1710    
1711            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1712    
1713            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1714                    which is implemented.
1715    
1716    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1717    
1718            * src/chm_common.c: coerce logical <-> double instead of
1719            typecasting;  needed for "l" matrix handling in cholmod.
1720    
1721            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1722    
1723            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1724            (Tsp2grNEL): other fixes needed
1725    
1726  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1727    
1728          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
# Line 7  Line 1732 
1732          * tests/: adaptions          * tests/: adaptions
1733          * src/chm_common.c (chm_dense_to_SEXP): and others:          * src/chm_common.c (chm_dense_to_SEXP): and others:
1734                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1735          * src/Csparse.c, etc: dito          * src/Csparse.c, etc: ditto
1736    
1737  2006-09-11  Douglas Bates  <bates@R-project.org>  2006-09-11  Douglas Bates  <bates@R-project.org>
1738    
# Line 26  Line 1751 
1751          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1752    
1753          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1754          * man/tcrossprod.Rd: dito          * man/tcrossprod.Rd: ditto
1755    
1756  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1757    
# Line 69  Line 1794 
1794    
1795          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1796          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1797          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
1798          * R/Csparse.R: dito          * R/Csparse.R: ditto
1799    
1800  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1801    
# Line 86  Line 1811 
1811    
1812          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1813          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1814          (.is.diagonal): dito          (.is.diagonal): ditto
1815    
1816          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1817    

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