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revision 1624, Wed Oct 11 15:00:11 2006 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>
817    
818            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
819    
820            * R/sparseVector.R: more *sparseVector coercions, notably for
821            non - double ones.
822    
823    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
824    
825            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
826              notably the new ones building on the new .Call(.)s:
827    
828            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
829            all 4 of [dlin]gCMatrix_colSums().
830    
831    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
832    
833            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
834            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
835              result
836    
837    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
838    
839            * R/kronecker.R: fix typo (could lead to inf.recursion)
840            * test/simple.R: testing that
841    
842            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
843            method as well (which can have arguments, show() can't).
844    
845    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
846    
847            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
848              added dgCMatrix_colSums for [col,row][Sums,Means]
849    
850    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
851    
852            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
853              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
854              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
855            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
856              class
857            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
858              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
859              row names to store the levels - duh!  Added an example.
860    
861    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
862    
863            * src/Csparse.c (Csparse_validate): check for *repeated* entries
864            thanks to example from Christian Buchta; with a test here:
865            * tests/simple.R:
866    
867    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
868    
869            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
870            of colSums(*, sparseResult = TRUE)
871    
872    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
873    
874            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
875            'na.rm = FALSE' as "everywhere" else in R.
876    
877    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
878    
879            * [r4421] src/CSparse_install.sh: Modify for new organization of
880              CSparse package
881            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
882              SuiteSparse
883            * [r4426] src/Makefile: add ./UFconfig to the include path for
884              compilation
885            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
886            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
887              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
888    
889    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
890    
891            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
892            * R/sparseMatrix.R (prSpMatrix): now gives a message about
893            suppressed column names.
894    
895    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
896    
897            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
898              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
899              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
900              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
901              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
902              Remove warnings after change to const char* CHAR
903    
904    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
905    
906            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
907              type of M_cholmod_ssmult
908    
909    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
910    
911            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
912              src/init.c: Yet another cholmod export - cholmod_ssmult
913    
914    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
915    
916            * NAMESPACE: exported drop0(), since
917            * man/drop0.Rd: I have seen several cases, I really wanted to use
918            it, so our users may want too.
919    
920    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
921    
922            * man/colSums.Rd: separately document colSums() etc, since these
923            have the extra argument 'sparseResult'.
924    
925    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
926    
927            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
928            * man/spMatrix.Rd: docu., including examples
929    
930            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
931            in order to make colMeans() etc fast *and* correct.
932            * R/sparseVector.R (replSPvec): "[<-" functionality for
933            sparseVectors; tested in
934            * tests/simple.R:
935    
936    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
937    
938            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
939            (very) sparse Matrices; output similar to Matlab's print().
940    
941    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
942    
943            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
944            0-based, indices (Jose Quesada <quesada@gmail.com>).
945    
946    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
947    
948            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
949    
950    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
951    
952            * R/Auxiliaries.R (sparsapply): new utility, much faster than
953            tapply1() for large sparse matrices.
954    
955    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
956    
957            * R/Matrix.R (dim<-): reshape now via sparseVector.
958    
959            * R/sparseVector.R: methods and function for
960            * R/AllClass.R: new "sparseVector" class and daughters.
961            * NAMESPACE: export new classes
962    
963    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
964    
965            * DESCRIPTION (Version): 0.99875-1
966            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
967    
968    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
969    
970            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
971            indexing
972            * tests/indexing.R: test set for that.
973    
974    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
975    
976            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
977            entries.
978            * tests/indexing.R(out): add regression test for it
979    
980    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
981    
982            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
983            name for "!" method definitions.
984    
985    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
986    
987            * R/Tsparse.R (intI): new utility, used for "[" :
988                    Cleanup up there, and fixes for duplicated indices - more TODO!
989    
990            * tests/indexing.R(out): more tests
991    
992    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
993    
994            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
995            code that is now part of the R Lapack library.
996    
997            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
998            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
999    
1000    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1001    
1002            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1003    
1004    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1005    
1006            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1007            up with extraneous names '0'...'<n-1>'
1008    
1009    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1010    
1011            * R/dgTMatrix.R (mat2dgT): care about NAs
1012    
1013    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1014    
1015            * R/kronecker.R: triangularity preserving methods
1016    
1017    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1018    
1019            * R/kronecker.R: new file collecting kronecker() methods in one
1020                    place.  Goal: become much faster!
1021    
1022    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1023    
1024            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1025            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1026            can be much faster.
1027    
1028            * tests/matprod.R: add regression tests for these (upper & lower).
1029    
1030    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1031    
1032            * R/Matrix.R (diff): method for our Matrices.
1033    
1034            * R/sparseMatrix.R (isDiagonal): check dim()!
1035    
1036    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1037    
1038            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1039            proposal from Tamas Papp.
1040    
1041    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1042    
1043            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1044    
1045            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1046            rather define and export  cBind() and rBind() only.
1047            --> useRs *must* change code that used to have cbind()/rbind() !!
1048    
1049            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1050            * R/bind.Rout.save: ditto
1051    
1052    2007-02-16  Douglas Bates  <bates@r-project.org>
1053    
1054            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1055            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1056            const modifier on declaration of the array 'valid'
1057    
1058    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1059    
1060            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1061    
1062    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1063    
1064            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1065    
1066            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1067            * tests/simple.R: test the above and some of these coercions:
1068    
1069            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1070                    be careful to avoid infinite recursion, using new coercions in
1071            * R/ngCMatrix.R and nsC... and ntC...
1072            * R/lsparseMatrix.R: ditto
1073    
1074            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1075    
1076            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1077            * R/Rsparse.R: reactivate .Call()s
1078    
1079            * tests/Class+Meth.R: a bit more on actual classes
1080    
1081    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1082    
1083            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1084    
1085    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1086    
1087            * DESCRIPTION (Version): 0.9975-10 to upload
1088    
1089            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1090            specific classes less unconditionally.
1091    
1092            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1093    
1094            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1095    
1096            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1097            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1098            R_to_CMatrix segfaults on one platform.
1099            Eliminate most coercion method to *specific* classes, and replace
1100            with virtual classes coercions.
1101    
1102    
1103    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1104    
1105            * src/init.c: export the CHM...._validate() placeholders, since
1106            they *are* called.
1107    
1108            * tests/Class+Meth.R (classCanCoerce): and starting to test
1109            all as(<from>, <to>)
1110    
1111    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1112    
1113            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1114            * tests/indexing.R: tested now
1115            * tests/indexing.Rout.save: updated
1116    
1117            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1118            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1119            appropriate.
1120    
1121            * NAMESPACE: export a trivial
1122            * R/Matrix.R: drop() Matrix-method
1123    
1124            * R/AllClass.R: moved all prototypes to virtual super classes.
1125    
1126            * R/Rsparse.R: many more coercions to have less exceptions in
1127            * tests/Class+Meth.R:
1128    
1129            * R/Ops.R (Compare): tweak for case with NA
1130            * tests/simpl.R: hence another 'FIXME' eliminated
1131    
1132    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1133    
1134            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1135            objects.
1136    
1137            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1138              and more of "!", "&", "|", all, any; coercions
1139    
1140            * R/Rsparse.R: many coercions (which enable quite a few other
1141            methods), thanks to enhancements in
1142            * src/dgCMatrix.c (R_to_CMatrix): new, and
1143            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1144            symmetric & triangular and ..RMatrix objects.
1145    
1146            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1147            renamed file from src/dsTMatrix.c;
1148            now dealing with symmetric and triangular Tsparse coercions, both
1149            to dense and general.
1150    
1151    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1152    
1153            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1154    
1155            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1156            where sensible when the <numeric> is of length > 1.
1157    
1158    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1159    
1160            * R/Matrix.R ([<-): for M[] <- value: fix length
1161    
1162    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1163    
1164            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1165            * R/ndenseMatrix.R: new coercions n* -> l*
1166    
1167    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1168    
1169            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1170    
1171            * R/Ops.R ("Logic"): and other "Ops", many updates
1172    
1173    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1174    
1175            * src/Mutils.h (SET_DimNames): new utility
1176    
1177            * R/Auxiliaries.R (nnzero): improved and now exported via
1178    
1179            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1180    
1181    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1182    
1183            * R/diagMatrix.R (!): fix typo.
1184    
1185    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1186    
1187            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1188                    allow to pass class definition --> speedup
1189            * R/sparseMatrix.R: apply the above
1190    
1191            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1192    
1193            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1194            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1195            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1196    
1197            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1198    
1199            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1200            and use it for "sparse*" as well, since it's faster than the
1201            as_Csparse(.) way.
1202    
1203    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1204    
1205            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1206    
1207    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1208    
1209            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1210            as method for   M[ ij ] <- v
1211            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1212    
1213            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1214            FALSE answer
1215    
1216            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1217            * tests/indexing.R: test it, and some of the above
1218    
1219    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1220    
1221            * R/Auxiliaries.R (is_duplicatedT): new utility
1222    
1223    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1224    
1225            * src/init.c (R_init_Matrix): export cholmod_scale
1226    
1227    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1228    
1229            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1230            base::as.matrix to (x, ...)
1231    
1232    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1233    
1234            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1235            file; start using "Logic", hence
1236    
1237            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1238            * NAMESPACE: import and export "Logic"
1239    
1240    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1241    
1242            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1243            only needed previously to R version 2.5.0.
1244    
1245    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1246    
1247            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1248    
1249            * R/Tsparse.R (replTmat): fix subassignment of triangular
1250            * R/Csparse.R (replCmat): ditto
1251            * tests/indexing.R: more tests, incl the above fix
1252    
1253    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1254    
1255            * R/Auxiliaries.R (drop0): extend for non CSparse
1256            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1257    
1258            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1259                    use uplo correctly (!); other places: use uplo_P() macro
1260    
1261            * R/Csparse.R (replCmat): call diagU2N() when needed
1262            * R/Tsparse.R (replTmat): ditto
1263    
1264            * src/dtCMatrix.c (tCMatrix_validate): new
1265            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1266            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1267    
1268            * R/diagMatrix.R (replDiag): to use in [<-
1269    
1270    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1271    
1272            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1273                    also more general diagU2N().
1274    
1275    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1276    
1277            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1278            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1279    
1280    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1281    
1282            * tests/bind.R: a few more cases
1283            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1284    
1285            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1286            * R/ddenseMatrix.R (cbind2/rbind2)
1287            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1288            * tests/indexing.R
1289            * tests/indexing.Rout.save: updated
1290    
1291    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1292    
1293            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1294            * tests/indexing.R
1295    
1296    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1297    
1298            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1299            align with proper position of "0", i.e., right for integers.
1300            argument 'align' by default is "fancy".
1301    
1302    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1303    
1304            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1305            * R/Csparse.R: and fix "Compare" for more cases.
1306            * tests/Class+Meth.R: test some of these (m == m, m != m)
1307    
1308    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1309    
1310            * R/lsparseMatrix.R: all() and any() methods
1311            * R/ldenseMatrix.R:      ditto
1312            * NAMESPACE, R/Matrix.R: ditto
1313    
1314            * man/all-methods.Rd: document them minimally
1315    
1316            * tests/simple.R: add a few examples for these
1317    
1318    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1319    
1320            * R/Tsparse.R ([): fix long standing typo in symmetric case
1321            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1322    
1323    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1324    
1325            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1326            to LL before converting to a sparse matrix. (The LDL form can be
1327            converted to a sparse matrix but it is implicitly a unit
1328            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1329    
1330    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1331    
1332            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1333    
1334    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1335    
1336            * DESCRIPTION (Version): updated -> release 0.9975-7
1337            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1338    
1339    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1340    
1341            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1342    
1343    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1344    
1345            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1346            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1347            is exactly singular.
1348    
1349    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1350    
1351            * DESCRIPTION (Date): updated -> release 0.9975-6
1352    
1353    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1354    
1355            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1356            now returns symmetric.
1357    
1358            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1359    
1360            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1361            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1362    
1363            * R/Auxiliaries.R (.type.kind): added
1364    
1365    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1366    
1367            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1368            running src/CSparse_install.sh
1369    
1370            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1371    
1372    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1373    
1374            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1375            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1376    
1377            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1378    
1379            * tests/Class+Meth.R (tstMatrixClass): now assure
1380            the (important in method programming) property :
1381    
1382                    ###>>  Every "Matrix" is either
1383                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1384    
1385                    (where "*" stands for "Matrix")
1386    
1387            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1388    
1389            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1390            * tests/validObj.R: checks for "comparison"
1391    
1392            * R/sparseMatrix.R ([): improved indexing for sparse;
1393                    trying to keep <symmetric>[ n, n] symmmetric
1394    
1395            * tests/indexing.R: indexing for logical sparse now ok
1396    
1397    
1398    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1399    
1400            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1401    
1402            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1403    
1404    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1405    
1406            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1407    
1408            * tests/simple.R: validObject() checking the above.
1409    
1410            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1411            replacing both dgCMatrix_validate and lgCM*.
1412    
1413            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1414            fix dimnames setting in other places.
1415            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1416    
1417    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1418    
1419            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1420    
1421            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1422            symmetry test, via
1423            * R/Auxiliaries.R (.as.dgC.0.factors):
1424    
1425    2006-11-01  Douglas Bates  <bates@r-project.org>
1426    
1427            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1428            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1429            <CsparseMatrix>) added
1430    
1431    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1432    
1433            * tests/matprod.R: add a variation of Harri's example
1434    
1435            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1436            recursive infinitely.
1437    
1438            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1439    
1440            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1441    
1442    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1443    
1444            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1445            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1446            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1447            satisfy the above test.
1448    
1449    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1450    
1451            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1452    
1453            * R/dgCMatrix.R: solve(a, b="missing") based on
1454            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1455            RHS = NULL.
1456    
1457            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1458            add more (needed) [t]crossprod() methods.
1459    
1460            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1461    
1462            * R/Auxiliaries.R (as_CspClass): cleanup
1463            (drop0): internal utility for "Csparse_drop(*, 0)"
1464            (.bail.out.2): encourage active feedback
1465    
1466    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1467    
1468            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1469    
1470            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1471            non-valid or 'sorted' case).
1472    
1473            * R/dsparseMatrix.R: add "chol" method.
1474            * R/ddenseMatrix.R: ditto
1475    
1476            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1477            * NAMESPACE (Ops)
1478            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1479            coercion; deprecating direct lower level coercions.
1480    
1481            * R/*.R (seq): use seq_len() and seq_along() where possible.
1482    
1483    
1484    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1485    
1486            * DESCRIPTION (Version): 0.9975-5 ready for release
1487    
1488    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1489    
1490            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1491    
1492    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1493    
1494            * R/AllClass.R (corMatrix): add 'validity' check;
1495                    comment out unused "LDL" class definition
1496            * NAMESPACE: mention, but do not export "LDL" class
1497            * R/corMatrix.R: new (simple), needed for R-devel with
1498            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1499              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1500    
1501    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1502    
1503            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1504            use Rprintf and R's error handling.
1505    
1506    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1507    
1508            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1509            * tests/matprod.R: add tests for the bug fixed.
1510    
1511  2006-10-11  Douglas Bates  <bates@stat.wisc.edu>  2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1512    
1513          * src/HBMM.[ch]: remove HarwellBoeing format for writing.          * src/HBMM.[ch]: remove HarwellBoeing format for writing.
# Line 5  Line 1515 
1515    
1516  2006-10-06  Douglas Bates  <bates@stat.wisc.edu>  2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1517    
1518          * R/dgCMatrix.R: deprecate the writeHB function.  Use writeMM instead.          * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1519    
1520  2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1521    

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