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revision 1922, Sat Jun 23 18:08:48 2007 UTC revision 2186, Mon Apr 28 12:37:01 2008 UTC
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1    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R ([): for triangularMatrix, check if result may be
4            triangular.
5            * tests/indexing.R: regression test
6    
7    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
10            * R/Ops.R: more methods, for lMatrix/nMatrix
11    
12    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/expm.R: new file for all expm() methods; notably new ones for
15            diagonal*, triangular*, symmetric* and also simple "matrix".
16    
17    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
20    
21            * inst/test-tools.R (assert.EQ.mat): better message when not equal
22    
23            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
24    
25            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
26            [dl]denseMatrix {identical slots; but more logical method dispatch}
27    
28    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
31    
32            * R/diagMatrix.R (determinant): method
33    
34    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
37    
38            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
39    
40            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
41            its diagonal
42    
43    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
46    
47            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
48    
49            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
50    
51            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
52    
53    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
56    
57            * R/Ops.R (.do.Logic.lsparse): fix NA case
58    
59            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
60    
61            * R/Auxiliaries.R (nnzero): fix special cases, using
62            * R/Auxiliaries.R (indDiag): new utility
63            * R/Auxiliaries.R (indTri): new argument 'diag'
64    
65            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
66    
67    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
70    
71            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
72            ".tCMatrix" triangular matrix.
73    
74            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
75            'clx' can be class *or* class representation.
76            (nnzSparse): new.
77            (non0ind): new 'xtendSymm' argument; used in
78            * R/Ops.R:
79    
80            * R/pMatrix.R: more efficient determinant() method
81    
82    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
85            * [disactivated] NAMESPACE: export(det)
86    
87            * R/diagMatrix.R (mkDiag): new substitute for diag()
88    
89            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
90            (as0, as1): new utility.
91    
92            * R/Csparse.R (diag, band): need diagU2N()
93    
94            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
95    
96            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
97    
98            * R/Ops.R (Compare): fix <nsp> o <nsp> case
99    
100            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
101    
102    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/Auxiliaries.R (signPerm): new utility for
105            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
106    
107            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
108            since we have our own error handler (and can use tryCatch() from R).
109    
110    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
113    
114            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
115            when not positive definite.
116    
117            * R/Auxiliaries.R (asTri): new auxiliary
118            (non0.i): make *much* faster for Tsparse with many non-zero
119            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
120    
121            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
122            test-tools.R , see below
123    
124            * R/dMatrix.R: fix "Summary" method: + diagU2N()
125    
126            * NAMESPACE, R/Matrix.R: add mean() method
127    
128    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
131            cold-hot colors; try *changed* default useAbs = FALSE
132            * man/image-methods.Rd:  nice examples
133    
134    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * inst/test-tools.R (checkMatrix): new function for modularizing part
137            of tstMatrixClass() in tests/Class+Meth.R
138    
139            * R/dsCMatrix.R: coercion from "matrix"
140            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
141    
142            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
143            add test for as(matrix(,0,0), <class>)
144    
145    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
148            work as determinant(matrix(,0,0)).
149    
150            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
151            * man/sparseLU-class.Rd: ditto
152    
153            * R/dgCMatrix.R (determinant): method building on lu()
154            * R/sparseMatrix.R, Matrix.R, ...: ditto
155    
156            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
157    
158    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
161            pattern matrices.
162    
163    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * src/dense.c (dense_to_Csparse): all declarations *before*
166            R_CheckStack(); needed e.g. for ancient gcc 2.96.
167    
168    
169    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * DESCRIPTION (Version): 0.999375-9 --- need to release
172            for R-devel (and R 2.7.0 alpha soon).
173    
174            * R/AllClass.R: drop "double" from "atomicVector" class union
175    
176            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
177            * R/dgeMatrix.R: ditto
178    
179            * R/sparseMatrix.R (summary): count NAs
180    
181            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
182    
183    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
186            order to become compatible to new R 2.7.0 base::rcond().
187    
188    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
191    
192            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
193    
194            * inst/test-tools.R (isValid): new utility, used much in
195            * tests/simple.R:
196    
197            * man/BunchKaufman-methods.Rd: added too
198    
199    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/dsyMatrix.R: add BunchKaufman() methods.
202            * R/dspMatrix.R:
203    
204            * src/init.c: add dsyMatrix_trf
205    
206    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
207    
208            * DESCRIPTION (Version): release 0.999375-7
209            * src/CHMfactor.c (CHMfactor_update): fix
210    
211    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
214            internal_chm_factor().
215    
216            * R/AllGeneric.R: do *not* define a "chol" generic
217                    (but rather use the implicit one *without* making pivot
218                    part of the signature)
219            * R/*.R: drop the 'pivot' from chol's signature and make
220                    'pivot=FALSE' a default argument of method definitions.
221    
222            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
223            version of Matrix
224    
225    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
228    
229            * R/sparseMatrix.R (is.na): new simple method
230            * R/denseMatrix.R (is.na): ditto.
231    
232            * R/diagMatrix.R (.symDiagonal): newly exported utility.
233    
234            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
235    
236            * src/UFsparse_download.sh: -->
237            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
238    
239    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
242            functionality; barely tested in
243            * tests/factorizing.R
244    
245            * src/Csparse.c (diag_tC): new functionality to enable faster
246            determinant(<dsCMatrix>, .) in
247            * R/dsCMatrix.R
248    
249    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
250    
251            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
252              src/CHMfactor.c, src/CHMfactor.h,
253              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
254              Log-determinant of the parent matrix from a CHMfactor object as
255              chm_factor_ldetL2; documentation and support
256    
257    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
260    
261    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
264            warning.
265    
266    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
268            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
269    
270            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
271              <diagonal> o <sparse_triangular>
272              setAs(., "nMatrix") added.
273    
274            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
275    
276            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
277                    new argument 'checkDense = FALSE'.
278    
279    
280    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
283            back-permutation of the matrix exponential.
284    
285            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
286    
287            * DESCRIPTION (Date,Version): ready to release 0.999375-5
288    
289            * tests/simple.R: testing diagN2U
290    
291    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/Auxiliaries.R (diagN2U): interface to
294    
295            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
296    
297            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
298    
299    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * src/chm_common.c (chm_diagN2U): new utility.
302    
303            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
304            make use of chm_diagN2U() and hence now preserve triangularity and
305            unit-triangularity.
306    
307            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
308    
309    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
312    
313            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
314            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
315    
316            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
317    
318            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
319    
320            * src/chm_common.c (AS_CHM_FINISH): add note about problem
321            for triangular (diag = "U").
322    
323    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
326            * R/bind.R:  .Call(dense_to_Csparse, *)
327    
328    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/Matrix.R (Matrix): no longer use coercions to specific classes
331                    (since we are discouraging them in user code).
332    
333            * tests/*.R: also replaces coercions to specific classes by
334            coercions to super classes.
335    
336            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
337    
338    
339    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
342    
343            * src/dense.c (dense_band): generalized from ddense_band
344    
345            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
346              now for "denseMatrix" (instead of just "ddense*"); much
347              simplified setMethod()s for these.
348    
349            * src/dense.c (dense_to_symmetric): generalized from ddense_*
350    
351    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
354            version of as(*, "symmetricMatric").
355    
356            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
357            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
358    
359    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/Matrix.R (subset.ij): utility, as first step to faster
362               M [ <ij-matrix> ] indexing.
363    
364            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
365    
366            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
367            for more efficient symmpart() and skewpart() methods.
368    
369            * src/Mutils.c (equal_string_vectors): utility
370    
371            * src/dense.c (ddense_to_symmetric): new function used in
372    
373            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
374    
375            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
376            order to match the generic (and evade .local(..)).
377    
378            * R/dsCMatrix.R: dgC -> dsC: use C code!
379    
380            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
381            as per TODO
382    
383            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
384    
385            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
386    
387    
388    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
391    
392            * R/Auxiliaries.R (non0.i): take out of non0ind
393    
394            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
395            make tril(), triu(), band() work for "matrix" and all "dense*"
396    
397            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
398            * tests/simple.R: test the fix above
399    
400            * R/sparseMatrix.R ([): simplification: no coerce to <general>
401                    before we use as(., <Tsparse>)[...] anyway
402    
403            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
404    
405            * R/triangularMatrix.R (isTriangular): methods for all subclasses
406            instead of "triangularMatrix" -- just to disambiguate
407    
408    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
411            * tests/indexing.R: example that fails above
412    
413    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
416            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
417                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
418    
419            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
420            * src/Tsparse.h, init.c: ditto
421            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
422                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
423            * R/sparseMatrix.R (isTriangular): hence simplified
424    
425    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/Ops.R (.Arith.Csparse): new utility factored out of former
428              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
429    
430    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
433    
434            * inst/test-tools.R (isOrthogonal): new function; also file restructured
435    
436    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
439            coercion to "nMatrix" and "pMatrix"
440    
441            * R/AllClass.R: "Schur" class;  "number" class union
442            * man/number-class.Rd:
443            * man/Schur-class.Rd:
444    
445            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
446            (.simpleSchur): Schur() method for diagonal matrices
447            (.triSchur):    Schur() method for triangular matrices
448            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
449    
450    
451    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
454    
455    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
458                    in order to ensure 'system = *' is not lost;
459                    formals()$system instead of cut&paste.
460            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
461    
462    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * DESCRIPTION (Date): make ready for release --> 0.999375-4
465    
466            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
467    
468    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
469    
470            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
471                    and hence does as.vector(.).
472            * man/pMatrix-class.Rd: docs
473            * R/sparseMatrix.R: fix for printing "integer sparse"
474    
475            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
476    
477            * R/Matrix.R and others: use "exact" function argument list for
478                    both "["   : (x, i,j, ..., drop)
479                    and  "[<-" : (x, i,j, ..., value)
480    
481            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
482            * R/Tsparse.R (replTmat):    ditto
483            * R/diagMatrix.R (replDiag): ditto
484            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
485            * tests/indexing.R: testing the above
486    
487    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
488    
489            * R/sparseMatrix.R (cov2cor): method for sparse matrices
490    
491            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
492    
493            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
494    
495            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
496    
497    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * R/Matrix.R: "generic" cov2cor() method
500    
501            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
502                    speed up Q %*% D %*% t(Q)
503            * tests/dpoMatrix.R: test nearPD()
504    
505    2007-12-05  Doug Bates and Martin Maechler
506    
507            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
508            stats::xtabs() allowing to create sparse matrices.
509    
510    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
511    
512            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
513    
514    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
517    
518    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/LU.R: solve() method for "denseLU"
521    
522    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
523    
524            * DESCRIPTION (Version): 0.999375-3 preparing for release
525    
526            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
527    
528            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
529    
530    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
531    
532            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
533              thanks to Kasper Kristensen.
534            * tests/matprod.R: regression test for that.
535    
536    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
537    
538            * [r4778] R/AllGeneric.R: Check R version before defining generics for
539              primitives
540    
541    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
542    
543            * R/denseMatrix.R (rcond): method
544            * R/sparseQR.R (rcond): method, use x or t(x)
545    
546    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
549            matrices.
550            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
551    
552            * man/rcond.Rd: mention the more general definition, and add
553            example for non-square matrices.
554    
555            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
556    
557    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
560    
561    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
564            * tests/indexing.R: add new regression for the above cases.
565    
566    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * src/Mutils.h (__sun): clause for alloca.h on Solaris
569    
570    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
571    
572            * DESCRIPTION (Date, Version): 0.999375-2
573    
574    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * R/HBMM.R (readMM): make work for pattern matrices as well
577    
578    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
579    
580            * [r4730] src/Mutils.h: declare alloca
581            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
582              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
583              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
584              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
585              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
586              methods; switch writeMM to use CHOLMOD code; repair readMM
587    
588    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
589    
590            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
591            Oehlschlaegel's ... result type still to be discussed!
592    
593    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * man/image-methods.Rd: new, combining all image() methods
596    
597    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
600            to work via dgC...
601    
602            * R/Matrix.R (Matrix): special treatment for "table" (S3)
603    
604    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
605    
606            * R/dgTMatrix.R (image): change defaults to
607                    aspect = "iso", colorkey = FALSE
608    
609    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
612            must copy its *expanded* x slot before LAPACK call.
613    
614            * tests/matprod.R: test the last days' changes.
615    
616    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
617    
618            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
619              as well as in sources
620            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
621              Lapack call
622    
623    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
624    
625            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
626                    ("Matrix", "matrix") which is needed in some cases.
627            Ditto for solve().
628    
629            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
630            infinite recursion in dispatch for some cases.
631    
632    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
633    
634            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
635              so pointers match
636    
637    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
638    
639            * DESCRIPTION (Date): set ready for release -- 0.999375-1
640    
641    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
642    
643            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
644              src/chm_common.c, src/chm_common.h: Change API for
645              numeric_as_chm_dense and N_AS_CHM_DN
646    
647    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
648    
649            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
650            * tests/matprod.R: regr.test for it
651    
652    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
653    
654            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
655            * tests/group-methods.R: and regression-test it
656    
657    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
658    
659            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
660              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
661              triplet_to_sparse, documentation, use typedefs
662    
663    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * man/dpoMatrix-class.Rd: added 'corMatrix' example
666    
667            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
668            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
669            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
670    
671            * R/lsparseMatrix.R: bug fix in "all" method
672            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
673    
674            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
675            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
676                    + matrix |-> nMatrix coercion
677            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
678            * man/pMatrix-class.Rd: ditto
679    
680            * R/Matrix.R (Summary): method for non-dMatrix
681    
682            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
683            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
684                    test all Summary methods.
685    
686    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
687    
688            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
689    
690    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
693    
694            * R/pMatrix.R (t?crossprod): methods for pMatrix
695    
696    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
697    
698            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
699    
700    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
701    
702            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
703              trying to fix a subtle bug - which has been somewhere else.
704    
705    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
706    
707            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
708              solve the bug
709    
710    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
711    
712            * src/dgCMatrix.c (compressed_to_TMatrix):
713    
714    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * src/Csparse.c (Rsparse_validate): new, to have some validity
717            checking for RsparseMatrix
718            * src/dgCMatrix.c (xRMatrix_validate): ditto
719            * src/dtCMatrix.c (tRMatrix_validate): ditto
720    
721    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
722    
723            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
724              lgRMatrix
725            * [r4568] DESCRIPTION: Prepare for bug-fix release
726            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
727              for declaration of cholmod_symmetry
728    
729    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
732            release.
733    
734    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
735    
736            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
737              functions - no longer used
738            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
739              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
740              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
741              Alloca
742    
743    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
744    
745            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
746              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
747              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
748              src/t_gCMatrix_colSums.c: more R_CheckStack()s
749    
750    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
751    
752            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
753              the required amount of memory then call M_numeric_as_chm_dense.
754            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
755              (like Calloc but calling alloca)
756    
757    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
760            and extended with more sophisticated 'col.names' option.
761            * NAMESPACE: export  printSparseMatrix()
762            * man/printSpMatrix.Rd: document, incl. examples
763    
764    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
765    
766            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
767              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
768              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
769    
770    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
771    
772            * DESCRIPTION (Version): 0.99875-4
773    
774            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
775            some dimnames perservation.
776    
777            * R/dsTMatrix.R (t-method): keep dimnames
778            * R/dtTMatrix.R:  ditto
779    
780            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
781            and ncol(.) < 10
782    
783            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
784            from Mutils.h
785    
786            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
787            e.g. in as(<ngCMatrix>, "matrix")
788    
789    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
790    
791            * [r4529] .: Create a branch for the API changes from the 0.99875
792              series to the 0.999375 series
793            * [r4530] DESCRIPTION, inst/include/Matrix.h,
794              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
795              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
796              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
797              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
798              as_cholmod_x functions
799    
800    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
801    
802            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
803              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
804              to Comparisons
805    
806    >>>>>>> .merge-right.r4561
807    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * DESCRIPTION (Version): 0.99875-3 ready to be released.
810    
811            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
812    
813            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
814            that should also work in a future version of R.
815    
816  2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
817    
818          * NAMESPACE, R/AllClass.R: "xsparseVector" class union.          * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
# Line 5  Line 820 
820          * R/sparseVector.R: more *sparseVector coercions, notably for          * R/sparseVector.R: more *sparseVector coercions, notably for
821          non - double ones.          non - double ones.
822    
   
823  2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
824    
825          * R/colSums.R: new file for all (col|row)(Sums|Means) methods,          * R/colSums.R: new file for all (col|row)(Sums|Means) methods,

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