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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 2115, Sat Feb 23 09:23:17 2008 UTC
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1    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
4            * R/bind.R:  .Call(dense_to_Csparse, *)
5    
6    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/Matrix.R (Matrix): no longer use coercions to specific classes
9                    (since we are discouraging them in user code).
10    
11            * tests/*.R: also replaces coercions to specific classes by
12            coercions to super classes.
13    
14            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
15    
16    
17    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
20    
21            * src/dense.c (dense_band): generalized from ddense_band
22    
23            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
24              now for "denseMatrix" (instead of just "ddense*"); much
25              simplified setMethod()s for these.
26    
27            * src/dense.c (dense_to_symmetric): generalized from ddense_*
28    
29    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
32            version of as(*, "symmetricMatric").
33    
34            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
35            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
36    
37    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/Matrix.R (subset.ij): utility, as first step to faster
40               M [ <ij-matrix> ] indexing.
41    
42            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
43    
44            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
45            for more efficient symmpart() and skewpart() methods.
46    
47            * src/Mutils.c (equal_string_vectors): utility
48    
49            * src/dense.c (ddense_to_symmetric): new function used in
50    
51            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
52    
53            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
54            order to match the generic (and evade .local(..)).
55    
56            * R/dsCMatrix.R: dgC -> dsC: use C code!
57    
58            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
59            as per TODO
60    
61            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
62    
63            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
64    
65    
66    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
69    
70            * R/Auxiliaries.R (non0.i): take out of non0ind
71    
72            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
73            make tril(), triu(), band() work for "matrix" and all "dense*"
74    
75            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
76            * tests/simple.R: test the fix above
77    
78            * R/sparseMatrix.R ([): simplification: no coerce to <general>
79                    before we use as(., <Tsparse>)[...] anyway
80    
81            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
82    
83            * R/triangularMatrix.R (isTriangular): methods for all subclasses
84            instead of "triangularMatrix" -- just to disambiguate
85    
86    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
89            * tests/indexing.R: example that fails above
90    
91    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
94            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
95                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
96    
97            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
98            * src/Tsparse.h, init.c: ditto
99            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
100                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
101            * R/sparseMatrix.R (isTriangular): hence simplified
102    
103    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/Ops.R (.Arith.Csparse): new utility factored out of former
106              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
107    
108    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
111    
112            * inst/test-tools.R (isOrthogonal): new function; also file restructured
113    
114    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
117            coercion to "nMatrix" and "pMatrix"
118    
119            * R/AllClass.R: "Schur" class;  "number" class union
120            * man/number-class.Rd:
121            * man/Schur-class.Rd:
122    
123            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
124            (.simpleSchur): Schur() method for diagonal matrices
125            (.triSchur):    Schur() method for triangular matrices
126            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
127    
128    
129    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
132    
133    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
136                    in order to ensure 'system = *' is not lost;
137                    formals()$system instead of cut&paste.
138            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
139    
140    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * DESCRIPTION (Date): make ready for release --> 0.999375-4
143    
144            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
145    
146    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
149                    and hence does as.vector(.).
150            * man/pMatrix-class.Rd: docs
151            * R/sparseMatrix.R: fix for printing "integer sparse"
152    
153            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
154    
155            * R/Matrix.R and others: use "exact" function argument list for
156                    both "["   : (x, i,j, ..., drop)
157                    and  "[<-" : (x, i,j, ..., value)
158    
159            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
160            * R/Tsparse.R (replTmat):    ditto
161            * R/diagMatrix.R (replDiag): ditto
162            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
163            * tests/indexing.R: testing the above
164    
165    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/sparseMatrix.R (cov2cor): method for sparse matrices
168    
169            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
170    
171            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
172    
173            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
174    
175    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/Matrix.R: "generic" cov2cor() method
178    
179            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
180                    speed up Q %*% D %*% t(Q)
181            * tests/dpoMatrix.R: test nearPD()
182    
183    2007-12-05  Doug Bates and Martin Maechler
184    
185            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
186            stats::xtabs() allowing to create sparse matrices.
187    
188    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
191    
192    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
195    
196    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * R/LU.R: solve() method for "denseLU"
199    
200    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * DESCRIPTION (Version): 0.999375-3 preparing for release
203    
204            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
205    
206            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
207    
208    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
211              thanks to Kasper Kristensen.
212            * tests/matprod.R: regression test for that.
213    
214    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
215    
216            * [r4778] R/AllGeneric.R: Check R version before defining generics for
217              primitives
218    
219    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/denseMatrix.R (rcond): method
222            * R/sparseQR.R (rcond): method, use x or t(x)
223    
224    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
227            matrices.
228            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
229    
230            * man/rcond.Rd: mention the more general definition, and add
231            example for non-square matrices.
232    
233            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
234    
235    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
238    
239    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
242            * tests/indexing.R: add new regression for the above cases.
243    
244    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * src/Mutils.h (__sun): clause for alloca.h on Solaris
247    
248    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * DESCRIPTION (Date, Version): 0.999375-2
251    
252    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/HBMM.R (readMM): make work for pattern matrices as well
255    
256    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
257    
258            * [r4730] src/Mutils.h: declare alloca
259            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
260              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
261              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
262              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
263              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
264              methods; switch writeMM to use CHOLMOD code; repair readMM
265    
266    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
268            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
269            Oehlschlaegel's ... result type still to be discussed!
270    
271    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * man/image-methods.Rd: new, combining all image() methods
274    
275    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
278            to work via dgC...
279    
280            * R/Matrix.R (Matrix): special treatment for "table" (S3)
281    
282    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/dgTMatrix.R (image): change defaults to
285                    aspect = "iso", colorkey = FALSE
286    
287    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
290            must copy its *expanded* x slot before LAPACK call.
291    
292            * tests/matprod.R: test the last days' changes.
293    
294    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
295    
296            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
297              as well as in sources
298            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
299              Lapack call
300    
301    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
304                    ("Matrix", "matrix") which is needed in some cases.
305            Ditto for solve().
306    
307            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
308            infinite recursion in dispatch for some cases.
309    
310    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
311    
312            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
313              so pointers match
314    
315    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * DESCRIPTION (Date): set ready for release -- 0.999375-1
318    
319    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
320    
321            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
322              src/chm_common.c, src/chm_common.h: Change API for
323              numeric_as_chm_dense and N_AS_CHM_DN
324    
325    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
328            * tests/matprod.R: regr.test for it
329    
330    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
333            * tests/group-methods.R: and regression-test it
334    
335    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
336    
337            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
338              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
339              triplet_to_sparse, documentation, use typedefs
340    
341    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * man/dpoMatrix-class.Rd: added 'corMatrix' example
344    
345            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
346            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
347            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
348    
349            * R/lsparseMatrix.R: bug fix in "all" method
350            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
351    
352            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
353            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
354                    + matrix |-> nMatrix coercion
355            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
356            * man/pMatrix-class.Rd: ditto
357    
358            * R/Matrix.R (Summary): method for non-dMatrix
359    
360            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
361            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
362                    test all Summary methods.
363    
364    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
367    
368    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
371    
372            * R/pMatrix.R (t?crossprod): methods for pMatrix
373    
374    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
375    
376            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
377    
378    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
379    
380            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
381              trying to fix a subtle bug - which has been somewhere else.
382    
383    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
384    
385            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
386              solve the bug
387    
388    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * src/dgCMatrix.c (compressed_to_TMatrix):
391    
392    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * src/Csparse.c (Rsparse_validate): new, to have some validity
395            checking for RsparseMatrix
396            * src/dgCMatrix.c (xRMatrix_validate): ditto
397            * src/dtCMatrix.c (tRMatrix_validate): ditto
398    
399    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
400    
401            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
402              lgRMatrix
403            * [r4568] DESCRIPTION: Prepare for bug-fix release
404            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
405              for declaration of cholmod_symmetry
406    
407    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
410            release.
411    
412    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
413    
414            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
415              functions - no longer used
416            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
417              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
418              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
419              Alloca
420    
421    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
422    
423            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
424              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
425              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
426              src/t_gCMatrix_colSums.c: more R_CheckStack()s
427    
428    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
429    
430            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
431              the required amount of memory then call M_numeric_as_chm_dense.
432            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
433              (like Calloc but calling alloca)
434    
435    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
438            and extended with more sophisticated 'col.names' option.
439            * NAMESPACE: export  printSparseMatrix()
440            * man/printSpMatrix.Rd: document, incl. examples
441    
442    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
443    
444            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
445              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
446              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
447    
448    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * DESCRIPTION (Version): 0.99875-4
451    
452            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
453            some dimnames perservation.
454    
455            * R/dsTMatrix.R (t-method): keep dimnames
456            * R/dtTMatrix.R:  ditto
457    
458            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
459            and ncol(.) < 10
460    
461            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
462            from Mutils.h
463    
464            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
465            e.g. in as(<ngCMatrix>, "matrix")
466    
467    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
468    
469            * [r4529] .: Create a branch for the API changes from the 0.99875
470              series to the 0.999375 series
471            * [r4530] DESCRIPTION, inst/include/Matrix.h,
472              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
473              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
474              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
475              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
476              as_cholmod_x functions
477    
478    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
479    
480            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
481              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
482              to Comparisons
483    
484    >>>>>>> .merge-right.r4561
485    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * DESCRIPTION (Version): 0.99875-3 ready to be released.
488    
489            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
490    
491            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
492            that should also work in a future version of R.
493    
494    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
497    
498            * R/sparseVector.R: more *sparseVector coercions, notably for
499            non - double ones.
500    
501    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
502    
503            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
504              notably the new ones building on the new .Call(.)s:
505    
506            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
507            all 4 of [dlin]gCMatrix_colSums().
508    
509    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
510    
511            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
512            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
513              result
514    
515    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
516    
517            * R/kronecker.R: fix typo (could lead to inf.recursion)
518            * test/simple.R: testing that
519    
520            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
521            method as well (which can have arguments, show() can't).
522    
523    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
524    
525            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
526              added dgCMatrix_colSums for [col,row][Sums,Means]
527    
528    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
529    
530            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
531              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
532              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
533            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
534              class
535            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
536              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
537              row names to store the levels - duh!  Added an example.
538    
539    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * src/Csparse.c (Csparse_validate): check for *repeated* entries
542            thanks to example from Christian Buchta; with a test here:
543            * tests/simple.R:
544    
545    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
546    
547            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
548            of colSums(*, sparseResult = TRUE)
549    
550    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
551    
552            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
553            'na.rm = FALSE' as "everywhere" else in R.
554    
555    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
556    
557            * [r4421] src/CSparse_install.sh: Modify for new organization of
558              CSparse package
559            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
560              SuiteSparse
561            * [r4426] src/Makefile: add ./UFconfig to the include path for
562              compilation
563            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
564            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
565              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
566    
567    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
568    
569            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
570            * R/sparseMatrix.R (prSpMatrix): now gives a message about
571            suppressed column names.
572    
573    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
574    
575            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
576              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
577              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
578              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
579              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
580              Remove warnings after change to const char* CHAR
581    
582    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
583    
584            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
585              type of M_cholmod_ssmult
586    
587    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
588    
589            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
590              src/init.c: Yet another cholmod export - cholmod_ssmult
591    
592    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * NAMESPACE: exported drop0(), since
595            * man/drop0.Rd: I have seen several cases, I really wanted to use
596            it, so our users may want too.
597    
598    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * man/colSums.Rd: separately document colSums() etc, since these
601            have the extra argument 'sparseResult'.
602    
603    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
605            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
606            * man/spMatrix.Rd: docu., including examples
607    
608            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
609            in order to make colMeans() etc fast *and* correct.
610            * R/sparseVector.R (replSPvec): "[<-" functionality for
611            sparseVectors; tested in
612            * tests/simple.R:
613    
614    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
617            (very) sparse Matrices; output similar to Matlab's print().
618    
619    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
620    
621            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
622            0-based, indices (Jose Quesada <quesada@gmail.com>).
623    
624    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
625    
626            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
627    
628    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
629    
630            * R/Auxiliaries.R (sparsapply): new utility, much faster than
631            tapply1() for large sparse matrices.
632    
633    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
634    
635            * R/Matrix.R (dim<-): reshape now via sparseVector.
636    
637            * R/sparseVector.R: methods and function for
638            * R/AllClass.R: new "sparseVector" class and daughters.
639            * NAMESPACE: export new classes
640    
641    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * DESCRIPTION (Version): 0.99875-1
644            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
645    
646    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
649            indexing
650            * tests/indexing.R: test set for that.
651    
652    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
653    
654            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
655            entries.
656            * tests/indexing.R(out): add regression test for it
657    
658    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
659    
660            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
661            name for "!" method definitions.
662    
663    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * R/Tsparse.R (intI): new utility, used for "[" :
666                    Cleanup up there, and fixes for duplicated indices - more TODO!
667    
668            * tests/indexing.R(out): more tests
669    
670    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
671    
672            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
673            code that is now part of the R Lapack library.
674    
675            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
676            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
677    
678    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
681    
682    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
685            up with extraneous names '0'...'<n-1>'
686    
687    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * R/dgTMatrix.R (mat2dgT): care about NAs
690    
691    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693            * R/kronecker.R: triangularity preserving methods
694    
695    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/kronecker.R: new file collecting kronecker() methods in one
698                    place.  Goal: become much faster!
699    
700    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
701    
702            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
703            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
704            can be much faster.
705    
706            * tests/matprod.R: add regression tests for these (upper & lower).
707    
708    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
709    
710            * R/Matrix.R (diff): method for our Matrices.
711    
712            * R/sparseMatrix.R (isDiagonal): check dim()!
713    
714    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * R/Matrix.R (dim<-): new method for "reshape()" built on a
717            proposal from Tamas Papp.
718    
719    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
722    
723            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
724            rather define and export  cBind() and rBind() only.
725            --> useRs *must* change code that used to have cbind()/rbind() !!
726    
727            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
728            * R/bind.Rout.save: ditto
729    
730    2007-02-16  Douglas Bates  <bates@r-project.org>
731    
732            * DESCRIPTION (Date, Version): 0.9975-11 with new date
733            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
734            const modifier on declaration of the array 'valid'
735    
736    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
737    
738            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
739    
740    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
741    
742            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
743    
744            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
745            * tests/simple.R: test the above and some of these coercions:
746    
747            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
748                    be careful to avoid infinite recursion, using new coercions in
749            * R/ngCMatrix.R and nsC... and ntC...
750            * R/lsparseMatrix.R: ditto
751    
752            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
753    
754            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
755            * R/Rsparse.R: reactivate .Call()s
756    
757            * tests/Class+Meth.R: a bit more on actual classes
758    
759    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
760    
761            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
762    
763    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * DESCRIPTION (Version): 0.9975-10 to upload
766    
767            * tests/Class+Meth.R (tstMatrixClass): require coercions to
768            specific classes less unconditionally.
769    
770            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
771    
772            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
773    
774            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
775            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
776            R_to_CMatrix segfaults on one platform.
777            Eliminate most coercion method to *specific* classes, and replace
778            with virtual classes coercions.
779    
780    
781    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
782    
783            * src/init.c: export the CHM...._validate() placeholders, since
784            they *are* called.
785    
786            * tests/Class+Meth.R (classCanCoerce): and starting to test
787            all as(<from>, <to>)
788    
789    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
792            * tests/indexing.R: tested now
793            * tests/indexing.Rout.save: updated
794    
795            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
796            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
797            appropriate.
798    
799            * NAMESPACE: export a trivial
800            * R/Matrix.R: drop() Matrix-method
801    
802            * R/AllClass.R: moved all prototypes to virtual super classes.
803    
804            * R/Rsparse.R: many more coercions to have less exceptions in
805            * tests/Class+Meth.R:
806    
807            * R/Ops.R (Compare): tweak for case with NA
808            * tests/simpl.R: hence another 'FIXME' eliminated
809    
810    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
811    
812            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
813            objects.
814    
815            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
816              and more of "!", "&", "|", all, any; coercions
817    
818            * R/Rsparse.R: many coercions (which enable quite a few other
819            methods), thanks to enhancements in
820            * src/dgCMatrix.c (R_to_CMatrix): new, and
821            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
822            symmetric & triangular and ..RMatrix objects.
823    
824            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
825            renamed file from src/dsTMatrix.c;
826            now dealing with symmetric and triangular Tsparse coercions, both
827            to dense and general.
828    
829    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
830    
831            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
832    
833            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
834            where sensible when the <numeric> is of length > 1.
835    
836    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
837    
838            * R/Matrix.R ([<-): for M[] <- value: fix length
839    
840    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
841    
842            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
843            * R/ndenseMatrix.R: new coercions n* -> l*
844    
845    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
846    
847            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
848    
849            * R/Ops.R ("Logic"): and other "Ops", many updates
850    
851    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
852    
853            * src/Mutils.h (SET_DimNames): new utility
854    
855            * R/Auxiliaries.R (nnzero): improved and now exported via
856    
857            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
858    
859    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
860    
861            * R/diagMatrix.R (!): fix typo.
862    
863    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
864    
865            * R/Auxiliaries.R (as_Csparse): and quite a few others:
866                    allow to pass class definition --> speedup
867            * R/sparseMatrix.R: apply the above
868    
869            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
870    
871            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
872            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
873            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
874    
875            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
876    
877            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
878            and use it for "sparse*" as well, since it's faster than the
879            as_Csparse(.) way.
880    
881    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
882    
883            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
884    
885    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
886    
887            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
888            as method for   M[ ij ] <- v
889            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
890    
891            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
892            FALSE answer
893    
894            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
895            * tests/indexing.R: test it, and some of the above
896    
897    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
898    
899            * R/Auxiliaries.R (is_duplicatedT): new utility
900    
901    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
902    
903            * src/init.c (R_init_Matrix): export cholmod_scale
904    
905    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
906    
907            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
908            base::as.matrix to (x, ...)
909    
910    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
911    
912            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
913            file; start using "Logic", hence
914    
915            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
916            * NAMESPACE: import and export "Logic"
917    
918    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
919    
920            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
921            only needed previously to R version 2.5.0.
922    
923    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
924    
925            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
926    
927            * R/Tsparse.R (replTmat): fix subassignment of triangular
928            * R/Csparse.R (replCmat): ditto
929            * tests/indexing.R: more tests, incl the above fix
930    
931    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
932    
933            * R/Auxiliaries.R (drop0): extend for non CSparse
934            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
935    
936            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
937                    use uplo correctly (!); other places: use uplo_P() macro
938    
939            * R/Csparse.R (replCmat): call diagU2N() when needed
940            * R/Tsparse.R (replTmat): ditto
941    
942            * src/dtCMatrix.c (tCMatrix_validate): new
943            * src/dtTMatrix.c (tTMatrix_validate): new, used in
944            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
945    
946            * R/diagMatrix.R (replDiag): to use in [<-
947    
948    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
949    
950            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
951                    also more general diagU2N().
952    
953    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
954    
955            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
956            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
957    
958    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
959    
960            * tests/bind.R: a few more cases
961            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
962    
963            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
964            * R/ddenseMatrix.R (cbind2/rbind2)
965            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
966            * tests/indexing.R
967            * tests/indexing.Rout.save: updated
968    
969    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
970    
971            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
972            * tests/indexing.R
973    
974    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
975    
976            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
977            align with proper position of "0", i.e., right for integers.
978            argument 'align' by default is "fancy".
979    
980    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
981    
982            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
983            * R/Csparse.R: and fix "Compare" for more cases.
984            * tests/Class+Meth.R: test some of these (m == m, m != m)
985    
986    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
987    
988            * R/lsparseMatrix.R: all() and any() methods
989            * R/ldenseMatrix.R:      ditto
990            * NAMESPACE, R/Matrix.R: ditto
991    
992            * man/all-methods.Rd: document them minimally
993    
994            * tests/simple.R: add a few examples for these
995    
996    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
997    
998            * R/Tsparse.R ([): fix long standing typo in symmetric case
999            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1000    
1001    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1002    
1003            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1004            to LL before converting to a sparse matrix. (The LDL form can be
1005            converted to a sparse matrix but it is implicitly a unit
1006            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1007    
1008    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1009    
1010            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1011    
1012    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1013    
1014            * DESCRIPTION (Version): updated -> release 0.9975-7
1015            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1016    
1017    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1018    
1019            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1020    
1021    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1022    
1023            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1024            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1025            is exactly singular.
1026    
1027    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1028    
1029            * DESCRIPTION (Date): updated -> release 0.9975-6
1030    
1031    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1032    
1033            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1034            now returns symmetric.
1035    
1036            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1037    
1038            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1039            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1040    
1041            * R/Auxiliaries.R (.type.kind): added
1042    
1043    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1044    
1045            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1046            running src/CSparse_install.sh
1047    
1048            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1049    
1050    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1051    
1052            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1053            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1054    
1055            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1056    
1057            * tests/Class+Meth.R (tstMatrixClass): now assure
1058            the (important in method programming) property :
1059    
1060                    ###>>  Every "Matrix" is either
1061                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1062    
1063                    (where "*" stands for "Matrix")
1064    
1065            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1066    
1067            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1068            * tests/validObj.R: checks for "comparison"
1069    
1070            * R/sparseMatrix.R ([): improved indexing for sparse;
1071                    trying to keep <symmetric>[ n, n] symmmetric
1072    
1073            * tests/indexing.R: indexing for logical sparse now ok
1074    
1075    
1076    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1077    
1078            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1079    
1080            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1081    
1082    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1083    
1084            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1085    
1086            * tests/simple.R: validObject() checking the above.
1087    
1088            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1089            replacing both dgCMatrix_validate and lgCM*.
1090    
1091            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1092            fix dimnames setting in other places.
1093            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1094    
1095    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1096    
1097            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1098    
1099            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1100            symmetry test, via
1101            * R/Auxiliaries.R (.as.dgC.0.factors):
1102    
1103    2006-11-01  Douglas Bates  <bates@r-project.org>
1104    
1105            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1106            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1107            <CsparseMatrix>) added
1108    
1109    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1110    
1111            * tests/matprod.R: add a variation of Harri's example
1112    
1113            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1114            recursive infinitely.
1115    
1116            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1117    
1118            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1119    
1120    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1121    
1122            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1123            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1124            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1125            satisfy the above test.
1126    
1127    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1128    
1129            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1130    
1131            * R/dgCMatrix.R: solve(a, b="missing") based on
1132            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1133            RHS = NULL.
1134    
1135            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1136            add more (needed) [t]crossprod() methods.
1137    
1138            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1139    
1140            * R/Auxiliaries.R (as_CspClass): cleanup
1141            (drop0): internal utility for "Csparse_drop(*, 0)"
1142            (.bail.out.2): encourage active feedback
1143    
1144    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1145    
1146            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1147    
1148            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1149            non-valid or 'sorted' case).
1150    
1151            * R/dsparseMatrix.R: add "chol" method.
1152            * R/ddenseMatrix.R: ditto
1153    
1154            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1155            * NAMESPACE (Ops)
1156            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1157            coercion; deprecating direct lower level coercions.
1158    
1159            * R/*.R (seq): use seq_len() and seq_along() where possible.
1160    
1161    
1162    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1163    
1164            * DESCRIPTION (Version): 0.9975-5 ready for release
1165    
1166    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1167    
1168            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1169    
1170    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1171    
1172            * R/AllClass.R (corMatrix): add 'validity' check;
1173                    comment out unused "LDL" class definition
1174            * NAMESPACE: mention, but do not export "LDL" class
1175            * R/corMatrix.R: new (simple), needed for R-devel with
1176            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1177              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1178    
1179    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1180    
1181            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1182            use Rprintf and R's error handling.
1183    
1184    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1185    
1186            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1187            * tests/matprod.R: add tests for the bug fixed.
1188    
1189    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1190    
1191            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1192            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1193    
1194    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1195    
1196            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1197    
1198    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1199    
1200            * DESCRIPTION (Version): 0.9975-3
1201    
1202            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1203            (sparse) matrices.
1204            * man/bdiag.Rd: docu + examples
1205    
1206            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1207    
1208            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1209            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1210    
1211            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1212            that result is sparse or diagonal (and not dense).
1213    
1214            * man/Subassign-methods.Rd: fix examples
1215    
1216            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1217            should always return a sparse (and not sometimes a diagonal) matrix.
1218    
1219    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1220    
1221            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1222    
1223    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1224    
1225            * DESCRIPTION (Version): 0.9975-2
1226    
1227            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1228    
1229    2006-10-02  Douglas Bates  <bates@R-project.org>
1230    
1231            * tests/dg_Matrix.R: Simplify test taking into account new code.
1232    
1233    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1234    
1235            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1236    
1237            * R/lsTMatrix.R: new files w/ missing methods
1238            * R/nsTMatrix.R:  "  'for completeness'
1239    
1240            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1241    
1242            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1243    
1244    
1245    2006-09-28  Douglas Bates  <bates@R-project.org>
1246    
1247            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1248            included.
1249    
1250            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1251            Export C-callable functions used in Zt_create in lme4.
1252    
1253    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1254    
1255            * DESCRIPTION (Version): 0.9975-1
1256    
1257            * tests/simple.R: less checks fail; using NA, found that our
1258                    kronecker() is not base-compatible with NA's.
1259    
1260            * R/dMatrix.R: "Compare" method now implemented for all cases
1261    
1262            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1263    
1264            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1265    
1266            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1267            * src/dspMatrix.c (dspMatrix_validate): ditto
1268    
1269            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1270              including coercion to [nl]tTMatrix.
1271    
1272            * R/diagMatrix.R (show): print a header line as for other classes.
1273    
1274    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1275    
1276            * src/Makefile.win (SUBDIRS): fix typo
1277    
1278    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1279    
1280            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1281    
1282    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1283    
1284            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1285            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1286            accept a symmetric matrix).
1287            * tests/group-methods.R: Uncomment test of crossprod applied to
1288            lsCMatrix objects.
1289    
1290    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1291    
1292            * R/AllClass.R (symmetricMatrix): add validity method (available
1293            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1294    
1295            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1296    
1297            * tests/indexing.Rout.save:
1298            * tests/indexing.R: additions, mainly for 'lsparse'
1299    
1300            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1301            case.
1302    
1303            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1304    
1305    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1306    
1307            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1308                    as 'N' (1-letter - Ok?)
1309    
1310            * tests/group-methods.R: add test for logical + NAs
1311    
1312            * R/dMatrix.R ("Compare"): fix to work with NA's
1313    
1314            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1315    
1316            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1317                    which is implemented.
1318    
1319    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1320    
1321            * src/chm_common.c: coerce logical <-> double instead of
1322            typecasting;  needed for "l" matrix handling in cholmod.
1323    
1324            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1325    
1326            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1327            (Tsp2grNEL): other fixes needed
1328    
1329    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1330    
1331            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1332                    Matrices, since "lMatrix", also "lsparseM" can have NA
1333            * R/ndenseMatrix.R, etc: new source files
1334            * man/nsparseMatrix-classes.Rd, etc: new help files
1335            * tests/: adaptions
1336            * src/chm_common.c (chm_dense_to_SEXP): and others:
1337                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1338            * src/Csparse.c, etc: ditto
1339    
1340    2006-09-11  Douglas Bates  <bates@R-project.org>
1341    
1342            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1343            alloc_d**Matrix functions to the lme4 package.
1344    
1345    2006-09-09  Douglas Bates  <bates@R-project.org>
1346    
1347            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1348            fixed
1349    
1350    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1351    
1352            * R/lMatrix.R: new
1353    
1354            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1355    
1356            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1357            * man/tcrossprod.Rd: ditto
1358    
1359    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1360    
1361            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1362            for exported functions
1363            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1364            Remove partitioning algorithms for sparse matrix reordering.  The
1365            copyright on the Metis code was problematic and the methods were
1366            rarely used.
1367            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1368            operations are now done entirely in CHOLMOD code.
1369    
1370    2006-09-06  Douglas Bates  <bates@R-project.org>
1371    
1372            * src/Mutils.h: Remove functions that are no longer used.
1373    
1374    2006-09-04  Douglas Bates  <bates@R-project.org>
1375    
1376            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1377            * src/DEPS.mkf: update
1378    
1379    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1380    
1381            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1382            * DESCRIPTION (Version): 0.9975-0
1383            (Depends): R (>= 2.4.0)
1384    
1385    2006-09-01  Douglas Bates  <bates@R-project.org>
1386    
1387            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1388    
1389    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1390    
1391            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1392            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1393    
1394            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1395    
1396    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1397    
1398            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1399            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1400            * R/dsparseMatrix.R: ditto
1401            * R/Csparse.R: ditto
1402    
1403    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1404    
1405            * R/dMatrix.R (Compare): improve availability of "<", etc
1406            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1407    
1408    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1409    
1410            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1411            of a 0-index which was used as 1-index (..hmm)
1412    
1413            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1414    
1415            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1416            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1417            (.is.diagonal): ditto
1418    
1419            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1420    
1421            * R/Matrix.R (Matrix): also work for NA data
1422    
1423  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1424    
1425          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting

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