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revision 1682, Fri Dec 1 18:42:40 2006 UTC revision 2196, Fri May 30 21:49:50 2008 UTC
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1    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
4            * tests/Simple.R: testing the above
5    
6    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
9    
10    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
13            * NAMESPACE (unname): finally exported
14    
15    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Auxiliaries.R (cholMat): possibly keep packed
18    
19            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
20            for R < 2.7.0.
21    
22            * R/Tsparse.R ([): for triangularMatrix, check if result may be
23            triangular.
24            * tests/indexing.R: regression test
25    
26    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
29            * R/Ops.R: more methods, for lMatrix/nMatrix
30    
31    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/expm.R: new file for all expm() methods; notably new ones for
34            diagonal*, triangular*, symmetric* and also simple "matrix".
35    
36    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
39    
40            * inst/test-tools.R (assert.EQ.mat): better message when not equal
41    
42            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
43    
44            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
45            [dl]denseMatrix {identical slots; but more logical method dispatch}
46    
47    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
50    
51            * R/diagMatrix.R (determinant): method
52    
53    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
56    
57            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
58    
59            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
60            its diagonal
61    
62    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
65    
66            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
67    
68            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
69    
70            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
71    
72    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
75    
76            * R/Ops.R (.do.Logic.lsparse): fix NA case
77    
78            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
79    
80            * R/Auxiliaries.R (nnzero): fix special cases, using
81            * R/Auxiliaries.R (indDiag): new utility
82            * R/Auxiliaries.R (indTri): new argument 'diag'
83    
84            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
85    
86    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
89    
90            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
91            ".tCMatrix" triangular matrix.
92    
93            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
94            'clx' can be class *or* class representation.
95            (nnzSparse): new.
96            (non0ind): new 'xtendSymm' argument; used in
97            * R/Ops.R:
98    
99            * R/pMatrix.R: more efficient determinant() method
100    
101    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
104            * [disactivated] NAMESPACE: export(det)
105    
106            * R/diagMatrix.R (mkDiag): new substitute for diag()
107    
108            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
109            (as0, as1): new utility.
110    
111            * R/Csparse.R (diag, band): need diagU2N()
112    
113            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
114    
115            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
116    
117            * R/Ops.R (Compare): fix <nsp> o <nsp> case
118    
119            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
120    
121    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/Auxiliaries.R (signPerm): new utility for
124            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
125    
126            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
127            since we have our own error handler (and can use tryCatch() from R).
128    
129    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
132    
133            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
134            when not positive definite.
135    
136            * R/Auxiliaries.R (asTri): new auxiliary
137            (non0.i): make *much* faster for Tsparse with many non-zero
138            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
139    
140            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
141            test-tools.R , see below
142    
143            * R/dMatrix.R: fix "Summary" method: + diagU2N()
144    
145            * NAMESPACE, R/Matrix.R: add mean() method
146    
147    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
150            cold-hot colors; try *changed* default useAbs = FALSE
151            * man/image-methods.Rd:  nice examples
152    
153    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * inst/test-tools.R (checkMatrix): new function for modularizing part
156            of tstMatrixClass() in tests/Class+Meth.R
157    
158            * R/dsCMatrix.R: coercion from "matrix"
159            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
160    
161            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
162            add test for as(matrix(,0,0), <class>)
163    
164    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
167            work as determinant(matrix(,0,0)).
168    
169            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
170            * man/sparseLU-class.Rd: ditto
171    
172            * R/dgCMatrix.R (determinant): method building on lu()
173            * R/sparseMatrix.R, Matrix.R, ...: ditto
174    
175            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
176    
177    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
180            pattern matrices.
181    
182    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * src/dense.c (dense_to_Csparse): all declarations *before*
185            R_CheckStack(); needed e.g. for ancient gcc 2.96.
186    
187    
188    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * DESCRIPTION (Version): 0.999375-9 --- need to release
191            for R-devel (and R 2.7.0 alpha soon).
192    
193            * R/AllClass.R: drop "double" from "atomicVector" class union
194    
195            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
196            * R/dgeMatrix.R: ditto
197    
198            * R/sparseMatrix.R (summary): count NAs
199    
200            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
201    
202    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
205            order to become compatible to new R 2.7.0 base::rcond().
206    
207    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
210    
211            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
212    
213            * inst/test-tools.R (isValid): new utility, used much in
214            * tests/simple.R:
215    
216            * man/BunchKaufman-methods.Rd: added too
217    
218    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/dsyMatrix.R: add BunchKaufman() methods.
221            * R/dspMatrix.R:
222    
223            * src/init.c: add dsyMatrix_trf
224    
225    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
226    
227            * DESCRIPTION (Version): release 0.999375-7
228            * src/CHMfactor.c (CHMfactor_update): fix
229    
230    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
233            internal_chm_factor().
234    
235            * R/AllGeneric.R: do *not* define a "chol" generic
236                    (but rather use the implicit one *without* making pivot
237                    part of the signature)
238            * R/*.R: drop the 'pivot' from chol's signature and make
239                    'pivot=FALSE' a default argument of method definitions.
240    
241            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
242            version of Matrix
243    
244    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
247    
248            * R/sparseMatrix.R (is.na): new simple method
249            * R/denseMatrix.R (is.na): ditto.
250    
251            * R/diagMatrix.R (.symDiagonal): newly exported utility.
252    
253            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
254    
255            * src/UFsparse_download.sh: -->
256            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
257    
258    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
261            functionality; barely tested in
262            * tests/factorizing.R
263    
264            * src/Csparse.c (diag_tC): new functionality to enable faster
265            determinant(<dsCMatrix>, .) in
266            * R/dsCMatrix.R
267    
268    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
269    
270            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
271              src/CHMfactor.c, src/CHMfactor.h,
272              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
273              Log-determinant of the parent matrix from a CHMfactor object as
274              chm_factor_ldetL2; documentation and support
275    
276    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
279    
280    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
283            warning.
284    
285    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
288    
289            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
290              <diagonal> o <sparse_triangular>
291              setAs(., "nMatrix") added.
292    
293            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
294    
295            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
296                    new argument 'checkDense = FALSE'.
297    
298    
299    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
302            back-permutation of the matrix exponential.
303    
304            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
305    
306            * DESCRIPTION (Date,Version): ready to release 0.999375-5
307    
308            * tests/simple.R: testing diagN2U
309    
310    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/Auxiliaries.R (diagN2U): interface to
313    
314            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
315    
316            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
317    
318    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * src/chm_common.c (chm_diagN2U): new utility.
321    
322            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
323            make use of chm_diagN2U() and hence now preserve triangularity and
324            unit-triangularity.
325    
326            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
327    
328    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
331    
332            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
333            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
334    
335            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
336    
337            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
338    
339            * src/chm_common.c (AS_CHM_FINISH): add note about problem
340            for triangular (diag = "U").
341    
342    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
345            * R/bind.R:  .Call(dense_to_Csparse, *)
346    
347    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * R/Matrix.R (Matrix): no longer use coercions to specific classes
350                    (since we are discouraging them in user code).
351    
352            * tests/*.R: also replaces coercions to specific classes by
353            coercions to super classes.
354    
355            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
356    
357    
358    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
361    
362            * src/dense.c (dense_band): generalized from ddense_band
363    
364            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
365              now for "denseMatrix" (instead of just "ddense*"); much
366              simplified setMethod()s for these.
367    
368            * src/dense.c (dense_to_symmetric): generalized from ddense_*
369    
370    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
373            version of as(*, "symmetricMatric").
374    
375            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
376            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
377    
378    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/Matrix.R (subset.ij): utility, as first step to faster
381               M [ <ij-matrix> ] indexing.
382    
383            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
384    
385            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
386            for more efficient symmpart() and skewpart() methods.
387    
388            * src/Mutils.c (equal_string_vectors): utility
389    
390            * src/dense.c (ddense_to_symmetric): new function used in
391    
392            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
393    
394            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
395            order to match the generic (and evade .local(..)).
396    
397            * R/dsCMatrix.R: dgC -> dsC: use C code!
398    
399            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
400            as per TODO
401    
402            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
403    
404            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
405    
406    
407    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
410    
411            * R/Auxiliaries.R (non0.i): take out of non0ind
412    
413            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
414            make tril(), triu(), band() work for "matrix" and all "dense*"
415    
416            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
417            * tests/simple.R: test the fix above
418    
419            * R/sparseMatrix.R ([): simplification: no coerce to <general>
420                    before we use as(., <Tsparse>)[...] anyway
421    
422            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
423    
424            * R/triangularMatrix.R (isTriangular): methods for all subclasses
425            instead of "triangularMatrix" -- just to disambiguate
426    
427    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
430            * tests/indexing.R: example that fails above
431    
432    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
435            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
436                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
437    
438            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
439            * src/Tsparse.h, init.c: ditto
440            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
441                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
442            * R/sparseMatrix.R (isTriangular): hence simplified
443    
444    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * R/Ops.R (.Arith.Csparse): new utility factored out of former
447              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
448    
449    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
452    
453            * inst/test-tools.R (isOrthogonal): new function; also file restructured
454    
455    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
458            coercion to "nMatrix" and "pMatrix"
459    
460            * R/AllClass.R: "Schur" class;  "number" class union
461            * man/number-class.Rd:
462            * man/Schur-class.Rd:
463    
464            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
465            (.simpleSchur): Schur() method for diagonal matrices
466            (.triSchur):    Schur() method for triangular matrices
467            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
468    
469    
470    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
473    
474    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
477                    in order to ensure 'system = *' is not lost;
478                    formals()$system instead of cut&paste.
479            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
480    
481    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
482    
483            * DESCRIPTION (Date): make ready for release --> 0.999375-4
484    
485            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
486    
487    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
488    
489            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
490                    and hence does as.vector(.).
491            * man/pMatrix-class.Rd: docs
492            * R/sparseMatrix.R: fix for printing "integer sparse"
493    
494            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
495    
496            * R/Matrix.R and others: use "exact" function argument list for
497                    both "["   : (x, i,j, ..., drop)
498                    and  "[<-" : (x, i,j, ..., value)
499    
500            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
501            * R/Tsparse.R (replTmat):    ditto
502            * R/diagMatrix.R (replDiag): ditto
503            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
504            * tests/indexing.R: testing the above
505    
506    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
507    
508            * R/sparseMatrix.R (cov2cor): method for sparse matrices
509    
510            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
511    
512            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
513    
514            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
515    
516    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
517    
518            * R/Matrix.R: "generic" cov2cor() method
519    
520            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
521                    speed up Q %*% D %*% t(Q)
522            * tests/dpoMatrix.R: test nearPD()
523    
524    2007-12-05  Doug Bates and Martin Maechler
525    
526            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
527            stats::xtabs() allowing to create sparse matrices.
528    
529    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
532    
533    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
536    
537    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * R/LU.R: solve() method for "denseLU"
540    
541    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
542    
543            * DESCRIPTION (Version): 0.999375-3 preparing for release
544    
545            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
546    
547            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
548    
549    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
552              thanks to Kasper Kristensen.
553            * tests/matprod.R: regression test for that.
554    
555    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
556    
557            * [r4778] R/AllGeneric.R: Check R version before defining generics for
558              primitives
559    
560    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * R/denseMatrix.R (rcond): method
563            * R/sparseQR.R (rcond): method, use x or t(x)
564    
565    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
568            matrices.
569            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
570    
571            * man/rcond.Rd: mention the more general definition, and add
572            example for non-square matrices.
573    
574            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
575    
576    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
579    
580    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
583            * tests/indexing.R: add new regression for the above cases.
584    
585    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * src/Mutils.h (__sun): clause for alloca.h on Solaris
588    
589    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * DESCRIPTION (Date, Version): 0.999375-2
592    
593    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * R/HBMM.R (readMM): make work for pattern matrices as well
596    
597    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
598    
599            * [r4730] src/Mutils.h: declare alloca
600            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
601              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
602              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
603              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
604              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
605              methods; switch writeMM to use CHOLMOD code; repair readMM
606    
607    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
610            Oehlschlaegel's ... result type still to be discussed!
611    
612    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * man/image-methods.Rd: new, combining all image() methods
615    
616    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
617    
618            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
619            to work via dgC...
620    
621            * R/Matrix.R (Matrix): special treatment for "table" (S3)
622    
623    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
624    
625            * R/dgTMatrix.R (image): change defaults to
626                    aspect = "iso", colorkey = FALSE
627    
628    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
629    
630            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
631            must copy its *expanded* x slot before LAPACK call.
632    
633            * tests/matprod.R: test the last days' changes.
634    
635    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
636    
637            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
638              as well as in sources
639            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
640              Lapack call
641    
642    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
643    
644            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
645                    ("Matrix", "matrix") which is needed in some cases.
646            Ditto for solve().
647    
648            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
649            infinite recursion in dispatch for some cases.
650    
651    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
652    
653            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
654              so pointers match
655    
656    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * DESCRIPTION (Date): set ready for release -- 0.999375-1
659    
660    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
661    
662            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
663              src/chm_common.c, src/chm_common.h: Change API for
664              numeric_as_chm_dense and N_AS_CHM_DN
665    
666    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
669            * tests/matprod.R: regr.test for it
670    
671    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
674            * tests/group-methods.R: and regression-test it
675    
676    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
677    
678            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
679              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
680              triplet_to_sparse, documentation, use typedefs
681    
682    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * man/dpoMatrix-class.Rd: added 'corMatrix' example
685    
686            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
687            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
688            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
689    
690            * R/lsparseMatrix.R: bug fix in "all" method
691            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
692    
693            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
694            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
695                    + matrix |-> nMatrix coercion
696            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
697            * man/pMatrix-class.Rd: ditto
698    
699            * R/Matrix.R (Summary): method for non-dMatrix
700    
701            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
702            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
703                    test all Summary methods.
704    
705    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
706    
707            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
708    
709    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
712    
713            * R/pMatrix.R (t?crossprod): methods for pMatrix
714    
715    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
716    
717            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
718    
719    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
720    
721            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
722              trying to fix a subtle bug - which has been somewhere else.
723    
724    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
725    
726            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
727              solve the bug
728    
729    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * src/dgCMatrix.c (compressed_to_TMatrix):
732    
733    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * src/Csparse.c (Rsparse_validate): new, to have some validity
736            checking for RsparseMatrix
737            * src/dgCMatrix.c (xRMatrix_validate): ditto
738            * src/dtCMatrix.c (tRMatrix_validate): ditto
739    
740    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
741    
742            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
743              lgRMatrix
744            * [r4568] DESCRIPTION: Prepare for bug-fix release
745            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
746              for declaration of cholmod_symmetry
747    
748    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
749    
750            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
751            release.
752    
753    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
754    
755            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
756              functions - no longer used
757            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
758              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
759              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
760              Alloca
761    
762    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
763    
764            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
765              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
766              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
767              src/t_gCMatrix_colSums.c: more R_CheckStack()s
768    
769    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
770    
771            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
772              the required amount of memory then call M_numeric_as_chm_dense.
773            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
774              (like Calloc but calling alloca)
775    
776    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
779            and extended with more sophisticated 'col.names' option.
780            * NAMESPACE: export  printSparseMatrix()
781            * man/printSpMatrix.Rd: document, incl. examples
782    
783    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
784    
785            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
786              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
787              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
788    
789    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * DESCRIPTION (Version): 0.99875-4
792    
793            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
794            some dimnames perservation.
795    
796            * R/dsTMatrix.R (t-method): keep dimnames
797            * R/dtTMatrix.R:  ditto
798    
799            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
800            and ncol(.) < 10
801    
802            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
803            from Mutils.h
804    
805            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
806            e.g. in as(<ngCMatrix>, "matrix")
807    
808    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
809    
810            * [r4529] .: Create a branch for the API changes from the 0.99875
811              series to the 0.999375 series
812            * [r4530] DESCRIPTION, inst/include/Matrix.h,
813              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
814              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
815              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
816              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
817              as_cholmod_x functions
818    
819    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
820    
821            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
822              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
823              to Comparisons
824    
825    >>>>>>> .merge-right.r4561
826    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
827    
828            * DESCRIPTION (Version): 0.99875-3 ready to be released.
829    
830            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
831    
832            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
833            that should also work in a future version of R.
834    
835    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
836    
837            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
838    
839            * R/sparseVector.R: more *sparseVector coercions, notably for
840            non - double ones.
841    
842    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
843    
844            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
845              notably the new ones building on the new .Call(.)s:
846    
847            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
848            all 4 of [dlin]gCMatrix_colSums().
849    
850    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
851    
852            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
853            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
854              result
855    
856    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
857    
858            * R/kronecker.R: fix typo (could lead to inf.recursion)
859            * test/simple.R: testing that
860    
861            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
862            method as well (which can have arguments, show() can't).
863    
864    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
865    
866            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
867              added dgCMatrix_colSums for [col,row][Sums,Means]
868    
869    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
870    
871            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
872              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
873              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
874            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
875              class
876            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
877              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
878              row names to store the levels - duh!  Added an example.
879    
880    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
881    
882            * src/Csparse.c (Csparse_validate): check for *repeated* entries
883            thanks to example from Christian Buchta; with a test here:
884            * tests/simple.R:
885    
886    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
887    
888            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
889            of colSums(*, sparseResult = TRUE)
890    
891    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
892    
893            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
894            'na.rm = FALSE' as "everywhere" else in R.
895    
896    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
897    
898            * [r4421] src/CSparse_install.sh: Modify for new organization of
899              CSparse package
900            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
901              SuiteSparse
902            * [r4426] src/Makefile: add ./UFconfig to the include path for
903              compilation
904            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
905            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
906              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
907    
908    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
909    
910            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
911            * R/sparseMatrix.R (prSpMatrix): now gives a message about
912            suppressed column names.
913    
914    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
915    
916            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
917              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
918              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
919              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
920              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
921              Remove warnings after change to const char* CHAR
922    
923    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
924    
925            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
926              type of M_cholmod_ssmult
927    
928    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
929    
930            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
931              src/init.c: Yet another cholmod export - cholmod_ssmult
932    
933    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
934    
935            * NAMESPACE: exported drop0(), since
936            * man/drop0.Rd: I have seen several cases, I really wanted to use
937            it, so our users may want too.
938    
939    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
940    
941            * man/colSums.Rd: separately document colSums() etc, since these
942            have the extra argument 'sparseResult'.
943    
944    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
945    
946            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
947            * man/spMatrix.Rd: docu., including examples
948    
949            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
950            in order to make colMeans() etc fast *and* correct.
951            * R/sparseVector.R (replSPvec): "[<-" functionality for
952            sparseVectors; tested in
953            * tests/simple.R:
954    
955    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
956    
957            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
958            (very) sparse Matrices; output similar to Matlab's print().
959    
960    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
961    
962            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
963            0-based, indices (Jose Quesada <quesada@gmail.com>).
964    
965    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
966    
967            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
968    
969    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
970    
971            * R/Auxiliaries.R (sparsapply): new utility, much faster than
972            tapply1() for large sparse matrices.
973    
974    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
975    
976            * R/Matrix.R (dim<-): reshape now via sparseVector.
977    
978            * R/sparseVector.R: methods and function for
979            * R/AllClass.R: new "sparseVector" class and daughters.
980            * NAMESPACE: export new classes
981    
982    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
983    
984            * DESCRIPTION (Version): 0.99875-1
985            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
986    
987    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
988    
989            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
990            indexing
991            * tests/indexing.R: test set for that.
992    
993    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
994    
995            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
996            entries.
997            * tests/indexing.R(out): add regression test for it
998    
999    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1000    
1001            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1002            name for "!" method definitions.
1003    
1004    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1005    
1006            * R/Tsparse.R (intI): new utility, used for "[" :
1007                    Cleanup up there, and fixes for duplicated indices - more TODO!
1008    
1009            * tests/indexing.R(out): more tests
1010    
1011    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1012    
1013            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1014            code that is now part of the R Lapack library.
1015    
1016            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1017            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1018    
1019    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
1021            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1022    
1023    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1024    
1025            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1026            up with extraneous names '0'...'<n-1>'
1027    
1028    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1029    
1030            * R/dgTMatrix.R (mat2dgT): care about NAs
1031    
1032    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1033    
1034            * R/kronecker.R: triangularity preserving methods
1035    
1036    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1037    
1038            * R/kronecker.R: new file collecting kronecker() methods in one
1039                    place.  Goal: become much faster!
1040    
1041    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1042    
1043            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1044            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1045            can be much faster.
1046    
1047            * tests/matprod.R: add regression tests for these (upper & lower).
1048    
1049    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1050    
1051            * R/Matrix.R (diff): method for our Matrices.
1052    
1053            * R/sparseMatrix.R (isDiagonal): check dim()!
1054    
1055    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1056    
1057            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1058            proposal from Tamas Papp.
1059    
1060    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1061    
1062            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1063    
1064            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1065            rather define and export  cBind() and rBind() only.
1066            --> useRs *must* change code that used to have cbind()/rbind() !!
1067    
1068            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1069            * R/bind.Rout.save: ditto
1070    
1071    2007-02-16  Douglas Bates  <bates@r-project.org>
1072    
1073            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1074            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1075            const modifier on declaration of the array 'valid'
1076    
1077    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1078    
1079            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1080    
1081    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1082    
1083            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1084    
1085            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1086            * tests/simple.R: test the above and some of these coercions:
1087    
1088            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1089                    be careful to avoid infinite recursion, using new coercions in
1090            * R/ngCMatrix.R and nsC... and ntC...
1091            * R/lsparseMatrix.R: ditto
1092    
1093            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1094    
1095            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1096            * R/Rsparse.R: reactivate .Call()s
1097    
1098            * tests/Class+Meth.R: a bit more on actual classes
1099    
1100    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1101    
1102            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1103    
1104    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1105    
1106            * DESCRIPTION (Version): 0.9975-10 to upload
1107    
1108            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1109            specific classes less unconditionally.
1110    
1111            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1112    
1113            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1114    
1115            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1116            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1117            R_to_CMatrix segfaults on one platform.
1118            Eliminate most coercion method to *specific* classes, and replace
1119            with virtual classes coercions.
1120    
1121    
1122    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1123    
1124            * src/init.c: export the CHM...._validate() placeholders, since
1125            they *are* called.
1126    
1127            * tests/Class+Meth.R (classCanCoerce): and starting to test
1128            all as(<from>, <to>)
1129    
1130    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1131    
1132            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1133            * tests/indexing.R: tested now
1134            * tests/indexing.Rout.save: updated
1135    
1136            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1137            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1138            appropriate.
1139    
1140            * NAMESPACE: export a trivial
1141            * R/Matrix.R: drop() Matrix-method
1142    
1143            * R/AllClass.R: moved all prototypes to virtual super classes.
1144    
1145            * R/Rsparse.R: many more coercions to have less exceptions in
1146            * tests/Class+Meth.R:
1147    
1148            * R/Ops.R (Compare): tweak for case with NA
1149            * tests/simpl.R: hence another 'FIXME' eliminated
1150    
1151    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1152    
1153            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1154            objects.
1155    
1156            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1157              and more of "!", "&", "|", all, any; coercions
1158    
1159            * R/Rsparse.R: many coercions (which enable quite a few other
1160            methods), thanks to enhancements in
1161            * src/dgCMatrix.c (R_to_CMatrix): new, and
1162            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1163            symmetric & triangular and ..RMatrix objects.
1164    
1165            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1166            renamed file from src/dsTMatrix.c;
1167            now dealing with symmetric and triangular Tsparse coercions, both
1168            to dense and general.
1169    
1170    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1171    
1172            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1173    
1174            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1175            where sensible when the <numeric> is of length > 1.
1176    
1177    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1178    
1179            * R/Matrix.R ([<-): for M[] <- value: fix length
1180    
1181    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1182    
1183            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1184            * R/ndenseMatrix.R: new coercions n* -> l*
1185    
1186    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1187    
1188            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1189    
1190            * R/Ops.R ("Logic"): and other "Ops", many updates
1191    
1192    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1193    
1194            * src/Mutils.h (SET_DimNames): new utility
1195    
1196            * R/Auxiliaries.R (nnzero): improved and now exported via
1197    
1198            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1199    
1200    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1201    
1202            * R/diagMatrix.R (!): fix typo.
1203    
1204    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1205    
1206            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1207                    allow to pass class definition --> speedup
1208            * R/sparseMatrix.R: apply the above
1209    
1210            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1211    
1212            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1213            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1214            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1215    
1216            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1217    
1218            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1219            and use it for "sparse*" as well, since it's faster than the
1220            as_Csparse(.) way.
1221    
1222    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1223    
1224            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1225    
1226    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1227    
1228            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1229            as method for   M[ ij ] <- v
1230            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1231    
1232            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1233            FALSE answer
1234    
1235            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1236            * tests/indexing.R: test it, and some of the above
1237    
1238    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1239    
1240            * R/Auxiliaries.R (is_duplicatedT): new utility
1241    
1242    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1243    
1244            * src/init.c (R_init_Matrix): export cholmod_scale
1245    
1246    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1247    
1248            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1249            base::as.matrix to (x, ...)
1250    
1251    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1252    
1253            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1254            file; start using "Logic", hence
1255    
1256            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1257            * NAMESPACE: import and export "Logic"
1258    
1259    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1260    
1261            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1262            only needed previously to R version 2.5.0.
1263    
1264    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1265    
1266            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1267    
1268            * R/Tsparse.R (replTmat): fix subassignment of triangular
1269            * R/Csparse.R (replCmat): ditto
1270            * tests/indexing.R: more tests, incl the above fix
1271    
1272    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1273    
1274            * R/Auxiliaries.R (drop0): extend for non CSparse
1275            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1276    
1277            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1278                    use uplo correctly (!); other places: use uplo_P() macro
1279    
1280            * R/Csparse.R (replCmat): call diagU2N() when needed
1281            * R/Tsparse.R (replTmat): ditto
1282    
1283            * src/dtCMatrix.c (tCMatrix_validate): new
1284            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1285            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1286    
1287            * R/diagMatrix.R (replDiag): to use in [<-
1288    
1289    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1290    
1291            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1292                    also more general diagU2N().
1293    
1294    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1295    
1296            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1297            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1298    
1299    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1300    
1301            * tests/bind.R: a few more cases
1302            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1303    
1304            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1305            * R/ddenseMatrix.R (cbind2/rbind2)
1306            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1307            * tests/indexing.R
1308            * tests/indexing.Rout.save: updated
1309    
1310    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1311    
1312            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1313            * tests/indexing.R
1314    
1315    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1316    
1317            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1318            align with proper position of "0", i.e., right for integers.
1319            argument 'align' by default is "fancy".
1320    
1321    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1322    
1323            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1324            * R/Csparse.R: and fix "Compare" for more cases.
1325            * tests/Class+Meth.R: test some of these (m == m, m != m)
1326    
1327    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1328    
1329            * R/lsparseMatrix.R: all() and any() methods
1330            * R/ldenseMatrix.R:      ditto
1331            * NAMESPACE, R/Matrix.R: ditto
1332    
1333            * man/all-methods.Rd: document them minimally
1334    
1335            * tests/simple.R: add a few examples for these
1336    
1337    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1338    
1339            * R/Tsparse.R ([): fix long standing typo in symmetric case
1340            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1341    
1342    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1343    
1344            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1345            to LL before converting to a sparse matrix. (The LDL form can be
1346            converted to a sparse matrix but it is implicitly a unit
1347            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1348    
1349    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1350    
1351            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1352    
1353    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1354    
1355            * DESCRIPTION (Version): updated -> release 0.9975-7
1356            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1357    
1358  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1359    
1360          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method

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