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revision 1507, Mon Sep 4 18:41:34 2006 UTC revision 2108, Fri Jan 25 11:14:32 2008 UTC
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1    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Ops.R (.Arith.Csparse): new utility factored out of former
4              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
5    
6    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
9    
10            * inst/test-tools.R (isOrthogonal): new function; also file restructured
11    
12    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
15            coercion to "nMatrix" and "pMatrix"
16    
17            * R/AllClass.R: "Schur" class;  "number" class union
18            * man/number-class.Rd:
19            * man/Schur-class.Rd:
20    
21            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
22            (.simpleSchur): Schur() method for diagonal matrices
23            (.triSchur):    Schur() method for triangular matrices
24            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
25    
26    
27    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
30    
31    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
34                    in order to ensure 'system = *' is not lost;
35                    formals()$system instead of cut&paste.
36            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
37    
38    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * DESCRIPTION (Date): make ready for release --> 0.999375-4
41    
42            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
43    
44    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
47                    and hence does as.vector(.).
48            * man/pMatrix-class.Rd: docs
49            * R/sparseMatrix.R: fix for printing "integer sparse"
50    
51            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
52    
53            * R/Matrix.R and others: use "exact" function argument list for
54                    both "["   : (x, i,j, ..., drop)
55                    and  "[<-" : (x, i,j, ..., value)
56    
57            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
58            * R/Tsparse.R (replTmat):    ditto
59            * R/diagMatrix.R (replDiag): ditto
60            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
61            * tests/indexing.R: testing the above
62    
63    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/sparseMatrix.R (cov2cor): method for sparse matrices
66    
67            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
68    
69            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
70    
71            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
72    
73    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/Matrix.R: "generic" cov2cor() method
76    
77            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
78                    speed up Q %*% D %*% t(Q)
79            * tests/dpoMatrix.R: test nearPD()
80    
81    2007-12-05  Doug Bates and Martin Maechler
82    
83            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
84            stats::xtabs() allowing to create sparse matrices.
85    
86    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
89    
90    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
93    
94    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/LU.R: solve() method for "denseLU"
97    
98    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * DESCRIPTION (Version): 0.999375-3 preparing for release
101    
102            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
103    
104            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
105    
106    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
109              thanks to Kasper Kristensen.
110            * tests/matprod.R: regression test for that.
111    
112    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
113    
114            * [r4778] R/AllGeneric.R: Check R version before defining generics for
115              primitives
116    
117    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/denseMatrix.R (rcond): method
120            * R/sparseQR.R (rcond): method, use x or t(x)
121    
122    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
125            matrices.
126            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
127    
128            * man/rcond.Rd: mention the more general definition, and add
129            example for non-square matrices.
130    
131            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
132    
133    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
136    
137    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
140            * tests/indexing.R: add new regression for the above cases.
141    
142    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * src/Mutils.h (__sun): clause for alloca.h on Solaris
145    
146    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * DESCRIPTION (Date, Version): 0.999375-2
149    
150    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/HBMM.R (readMM): make work for pattern matrices as well
153    
154    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
155    
156            * [r4730] src/Mutils.h: declare alloca
157            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
158              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
159              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
160              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
161              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
162              methods; switch writeMM to use CHOLMOD code; repair readMM
163    
164    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
167            Oehlschlaegel's ... result type still to be discussed!
168    
169    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * man/image-methods.Rd: new, combining all image() methods
172    
173    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
176            to work via dgC...
177    
178            * R/Matrix.R (Matrix): special treatment for "table" (S3)
179    
180    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/dgTMatrix.R (image): change defaults to
183                    aspect = "iso", colorkey = FALSE
184    
185    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
188            must copy its *expanded* x slot before LAPACK call.
189    
190            * tests/matprod.R: test the last days' changes.
191    
192    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
193    
194            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
195              as well as in sources
196            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
197              Lapack call
198    
199    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
202                    ("Matrix", "matrix") which is needed in some cases.
203            Ditto for solve().
204    
205            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
206            infinite recursion in dispatch for some cases.
207    
208    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
209    
210            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
211              so pointers match
212    
213    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * DESCRIPTION (Date): set ready for release -- 0.999375-1
216    
217    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
218    
219            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
220              src/chm_common.c, src/chm_common.h: Change API for
221              numeric_as_chm_dense and N_AS_CHM_DN
222    
223    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
226            * tests/matprod.R: regr.test for it
227    
228    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
231            * tests/group-methods.R: and regression-test it
232    
233    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
234    
235            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
236              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
237              triplet_to_sparse, documentation, use typedefs
238    
239    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * man/dpoMatrix-class.Rd: added 'corMatrix' example
242    
243            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
244            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
245            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
246    
247            * R/lsparseMatrix.R: bug fix in "all" method
248            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
249    
250            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
251            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
252                    + matrix |-> nMatrix coercion
253            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
254            * man/pMatrix-class.Rd: ditto
255    
256            * R/Matrix.R (Summary): method for non-dMatrix
257    
258            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
259            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
260                    test all Summary methods.
261    
262    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
265    
266    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
268            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
269    
270            * R/pMatrix.R (t?crossprod): methods for pMatrix
271    
272    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
273    
274            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
275    
276    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
277    
278            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
279              trying to fix a subtle bug - which has been somewhere else.
280    
281    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
282    
283            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
284              solve the bug
285    
286    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * src/dgCMatrix.c (compressed_to_TMatrix):
289    
290    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * src/Csparse.c (Rsparse_validate): new, to have some validity
293            checking for RsparseMatrix
294            * src/dgCMatrix.c (xRMatrix_validate): ditto
295            * src/dtCMatrix.c (tRMatrix_validate): ditto
296    
297    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
298    
299            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
300              lgRMatrix
301            * [r4568] DESCRIPTION: Prepare for bug-fix release
302            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
303              for declaration of cholmod_symmetry
304    
305    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
308            release.
309    
310    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
311    
312            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
313              functions - no longer used
314            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
315              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
316              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
317              Alloca
318    
319    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
320    
321            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
322              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
323              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
324              src/t_gCMatrix_colSums.c: more R_CheckStack()s
325    
326    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
327    
328            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
329              the required amount of memory then call M_numeric_as_chm_dense.
330            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
331              (like Calloc but calling alloca)
332    
333    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
336            and extended with more sophisticated 'col.names' option.
337            * NAMESPACE: export  printSparseMatrix()
338            * man/printSpMatrix.Rd: document, incl. examples
339    
340    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
341    
342            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
343              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
344              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
345    
346    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * DESCRIPTION (Version): 0.99875-4
349    
350            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
351            some dimnames perservation.
352    
353            * R/dsTMatrix.R (t-method): keep dimnames
354            * R/dtTMatrix.R:  ditto
355    
356            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
357            and ncol(.) < 10
358    
359            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
360            from Mutils.h
361    
362            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
363            e.g. in as(<ngCMatrix>, "matrix")
364    
365    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
366    
367            * [r4529] .: Create a branch for the API changes from the 0.99875
368              series to the 0.999375 series
369            * [r4530] DESCRIPTION, inst/include/Matrix.h,
370              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
371              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
372              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
373              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
374              as_cholmod_x functions
375    
376    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
377    
378            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
379              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
380              to Comparisons
381    
382    >>>>>>> .merge-right.r4561
383    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * DESCRIPTION (Version): 0.99875-3 ready to be released.
386    
387            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
388    
389            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
390            that should also work in a future version of R.
391    
392    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
395    
396            * R/sparseVector.R: more *sparseVector coercions, notably for
397            non - double ones.
398    
399    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
402              notably the new ones building on the new .Call(.)s:
403    
404            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
405            all 4 of [dlin]gCMatrix_colSums().
406    
407    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
408    
409            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
410            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
411              result
412    
413    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/kronecker.R: fix typo (could lead to inf.recursion)
416            * test/simple.R: testing that
417    
418            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
419            method as well (which can have arguments, show() can't).
420    
421    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
422    
423            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
424              added dgCMatrix_colSums for [col,row][Sums,Means]
425    
426    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
427    
428            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
429              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
430              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
431            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
432              class
433            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
434              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
435              row names to store the levels - duh!  Added an example.
436    
437    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
438    
439            * src/Csparse.c (Csparse_validate): check for *repeated* entries
440            thanks to example from Christian Buchta; with a test here:
441            * tests/simple.R:
442    
443    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
444    
445            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
446            of colSums(*, sparseResult = TRUE)
447    
448    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
451            'na.rm = FALSE' as "everywhere" else in R.
452    
453    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
454    
455            * [r4421] src/CSparse_install.sh: Modify for new organization of
456              CSparse package
457            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
458              SuiteSparse
459            * [r4426] src/Makefile: add ./UFconfig to the include path for
460              compilation
461            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
462            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
463              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
464    
465    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
468            * R/sparseMatrix.R (prSpMatrix): now gives a message about
469            suppressed column names.
470    
471    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
472    
473            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
474              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
475              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
476              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
477              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
478              Remove warnings after change to const char* CHAR
479    
480    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
481    
482            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
483              type of M_cholmod_ssmult
484    
485    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
486    
487            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
488              src/init.c: Yet another cholmod export - cholmod_ssmult
489    
490    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * NAMESPACE: exported drop0(), since
493            * man/drop0.Rd: I have seen several cases, I really wanted to use
494            it, so our users may want too.
495    
496    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * man/colSums.Rd: separately document colSums() etc, since these
499            have the extra argument 'sparseResult'.
500    
501    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
502    
503            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
504            * man/spMatrix.Rd: docu., including examples
505    
506            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
507            in order to make colMeans() etc fast *and* correct.
508            * R/sparseVector.R (replSPvec): "[<-" functionality for
509            sparseVectors; tested in
510            * tests/simple.R:
511    
512    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
515            (very) sparse Matrices; output similar to Matlab's print().
516    
517    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
518    
519            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
520            0-based, indices (Jose Quesada <quesada@gmail.com>).
521    
522    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
523    
524            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
525    
526    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
527    
528            * R/Auxiliaries.R (sparsapply): new utility, much faster than
529            tapply1() for large sparse matrices.
530    
531    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
532    
533            * R/Matrix.R (dim<-): reshape now via sparseVector.
534    
535            * R/sparseVector.R: methods and function for
536            * R/AllClass.R: new "sparseVector" class and daughters.
537            * NAMESPACE: export new classes
538    
539    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * DESCRIPTION (Version): 0.99875-1
542            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
543    
544    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
545    
546            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
547            indexing
548            * tests/indexing.R: test set for that.
549    
550    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
551    
552            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
553            entries.
554            * tests/indexing.R(out): add regression test for it
555    
556    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
559            name for "!" method definitions.
560    
561    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/Tsparse.R (intI): new utility, used for "[" :
564                    Cleanup up there, and fixes for duplicated indices - more TODO!
565    
566            * tests/indexing.R(out): more tests
567    
568    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
569    
570            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
571            code that is now part of the R Lapack library.
572    
573            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
574            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
575    
576    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
579    
580    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
583            up with extraneous names '0'...'<n-1>'
584    
585    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * R/dgTMatrix.R (mat2dgT): care about NAs
588    
589    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * R/kronecker.R: triangularity preserving methods
592    
593    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * R/kronecker.R: new file collecting kronecker() methods in one
596                    place.  Goal: become much faster!
597    
598    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
601            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
602            can be much faster.
603    
604            * tests/matprod.R: add regression tests for these (upper & lower).
605    
606    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * R/Matrix.R (diff): method for our Matrices.
609    
610            * R/sparseMatrix.R (isDiagonal): check dim()!
611    
612    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * R/Matrix.R (dim<-): new method for "reshape()" built on a
615            proposal from Tamas Papp.
616    
617    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
618    
619            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
620    
621            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
622            rather define and export  cBind() and rBind() only.
623            --> useRs *must* change code that used to have cbind()/rbind() !!
624    
625            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
626            * R/bind.Rout.save: ditto
627    
628    2007-02-16  Douglas Bates  <bates@r-project.org>
629    
630            * DESCRIPTION (Date, Version): 0.9975-11 with new date
631            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
632            const modifier on declaration of the array 'valid'
633    
634    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
635    
636            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
637    
638    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
639    
640            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
641    
642            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
643            * tests/simple.R: test the above and some of these coercions:
644    
645            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
646                    be careful to avoid infinite recursion, using new coercions in
647            * R/ngCMatrix.R and nsC... and ntC...
648            * R/lsparseMatrix.R: ditto
649    
650            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
651    
652            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
653            * R/Rsparse.R: reactivate .Call()s
654    
655            * tests/Class+Meth.R: a bit more on actual classes
656    
657    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
658    
659            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
660    
661    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
662    
663            * DESCRIPTION (Version): 0.9975-10 to upload
664    
665            * tests/Class+Meth.R (tstMatrixClass): require coercions to
666            specific classes less unconditionally.
667    
668            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
669    
670            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
671    
672            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
673            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
674            R_to_CMatrix segfaults on one platform.
675            Eliminate most coercion method to *specific* classes, and replace
676            with virtual classes coercions.
677    
678    
679    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
680    
681            * src/init.c: export the CHM...._validate() placeholders, since
682            they *are* called.
683    
684            * tests/Class+Meth.R (classCanCoerce): and starting to test
685            all as(<from>, <to>)
686    
687    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
690            * tests/indexing.R: tested now
691            * tests/indexing.Rout.save: updated
692    
693            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
694            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
695            appropriate.
696    
697            * NAMESPACE: export a trivial
698            * R/Matrix.R: drop() Matrix-method
699    
700            * R/AllClass.R: moved all prototypes to virtual super classes.
701    
702            * R/Rsparse.R: many more coercions to have less exceptions in
703            * tests/Class+Meth.R:
704    
705            * R/Ops.R (Compare): tweak for case with NA
706            * tests/simpl.R: hence another 'FIXME' eliminated
707    
708    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
709    
710            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
711            objects.
712    
713            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
714              and more of "!", "&", "|", all, any; coercions
715    
716            * R/Rsparse.R: many coercions (which enable quite a few other
717            methods), thanks to enhancements in
718            * src/dgCMatrix.c (R_to_CMatrix): new, and
719            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
720            symmetric & triangular and ..RMatrix objects.
721    
722            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
723            renamed file from src/dsTMatrix.c;
724            now dealing with symmetric and triangular Tsparse coercions, both
725            to dense and general.
726    
727    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
730    
731            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
732            where sensible when the <numeric> is of length > 1.
733    
734    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
735    
736            * R/Matrix.R ([<-): for M[] <- value: fix length
737    
738    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
739    
740            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
741            * R/ndenseMatrix.R: new coercions n* -> l*
742    
743    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
744    
745            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
746    
747            * R/Ops.R ("Logic"): and other "Ops", many updates
748    
749    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
750    
751            * src/Mutils.h (SET_DimNames): new utility
752    
753            * R/Auxiliaries.R (nnzero): improved and now exported via
754    
755            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
756    
757    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * R/diagMatrix.R (!): fix typo.
760    
761    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * R/Auxiliaries.R (as_Csparse): and quite a few others:
764                    allow to pass class definition --> speedup
765            * R/sparseMatrix.R: apply the above
766    
767            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
768    
769            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
770            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
771            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
772    
773            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
774    
775            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
776            and use it for "sparse*" as well, since it's faster than the
777            as_Csparse(.) way.
778    
779    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
780    
781            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
782    
783    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
784    
785            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
786            as method for   M[ ij ] <- v
787            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
788    
789            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
790            FALSE answer
791    
792            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
793            * tests/indexing.R: test it, and some of the above
794    
795    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * R/Auxiliaries.R (is_duplicatedT): new utility
798    
799    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
800    
801            * src/init.c (R_init_Matrix): export cholmod_scale
802    
803    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
804    
805            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
806            base::as.matrix to (x, ...)
807    
808    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
809    
810            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
811            file; start using "Logic", hence
812    
813            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
814            * NAMESPACE: import and export "Logic"
815    
816    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
817    
818            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
819            only needed previously to R version 2.5.0.
820    
821    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
822    
823            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
824    
825            * R/Tsparse.R (replTmat): fix subassignment of triangular
826            * R/Csparse.R (replCmat): ditto
827            * tests/indexing.R: more tests, incl the above fix
828    
829    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
830    
831            * R/Auxiliaries.R (drop0): extend for non CSparse
832            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
833    
834            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
835                    use uplo correctly (!); other places: use uplo_P() macro
836    
837            * R/Csparse.R (replCmat): call diagU2N() when needed
838            * R/Tsparse.R (replTmat): ditto
839    
840            * src/dtCMatrix.c (tCMatrix_validate): new
841            * src/dtTMatrix.c (tTMatrix_validate): new, used in
842            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
843    
844            * R/diagMatrix.R (replDiag): to use in [<-
845    
846    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
847    
848            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
849                    also more general diagU2N().
850    
851    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
852    
853            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
854            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
855    
856    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
857    
858            * tests/bind.R: a few more cases
859            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
860    
861            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
862            * R/ddenseMatrix.R (cbind2/rbind2)
863            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
864            * tests/indexing.R
865            * tests/indexing.Rout.save: updated
866    
867    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
868    
869            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
870            * tests/indexing.R
871    
872    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
873    
874            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
875            align with proper position of "0", i.e., right for integers.
876            argument 'align' by default is "fancy".
877    
878    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
881            * R/Csparse.R: and fix "Compare" for more cases.
882            * tests/Class+Meth.R: test some of these (m == m, m != m)
883    
884    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
885    
886            * R/lsparseMatrix.R: all() and any() methods
887            * R/ldenseMatrix.R:      ditto
888            * NAMESPACE, R/Matrix.R: ditto
889    
890            * man/all-methods.Rd: document them minimally
891    
892            * tests/simple.R: add a few examples for these
893    
894    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
895    
896            * R/Tsparse.R ([): fix long standing typo in symmetric case
897            * man/dsCMatrix-class.Rd: add example exhibiting the above case
898    
899    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
900    
901            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
902            to LL before converting to a sparse matrix. (The LDL form can be
903            converted to a sparse matrix but it is implicitly a unit
904            triangular matrix and a diagonal matrix overwritten on the diagonal.)
905    
906    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
907    
908            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
909    
910    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
911    
912            * DESCRIPTION (Version): updated -> release 0.9975-7
913            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
914    
915    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
916    
917            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
918    
919    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
920    
921            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
922            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
923            is exactly singular.
924    
925    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
926    
927            * DESCRIPTION (Date): updated -> release 0.9975-6
928    
929    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
930    
931            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
932            now returns symmetric.
933    
934            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
935    
936            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
937            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
938    
939            * R/Auxiliaries.R (.type.kind): added
940    
941    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
942    
943            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
944            running src/CSparse_install.sh
945    
946            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
947    
948    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
949    
950            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
951            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
952    
953            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
954    
955            * tests/Class+Meth.R (tstMatrixClass): now assure
956            the (important in method programming) property :
957    
958                    ###>>  Every "Matrix" is either
959                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
960    
961                    (where "*" stands for "Matrix")
962    
963            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
964    
965            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
966            * tests/validObj.R: checks for "comparison"
967    
968            * R/sparseMatrix.R ([): improved indexing for sparse;
969                    trying to keep <symmetric>[ n, n] symmmetric
970    
971            * tests/indexing.R: indexing for logical sparse now ok
972    
973    
974    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
975    
976            * src/Tsparse.c: use xTsparse_validate() , and hence remove
977    
978            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
979    
980    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
981    
982            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
983    
984            * tests/simple.R: validObject() checking the above.
985    
986            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
987            replacing both dgCMatrix_validate and lgCM*.
988    
989            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
990            fix dimnames setting in other places.
991            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
992    
993    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
994    
995            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
996    
997            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
998            symmetry test, via
999            * R/Auxiliaries.R (.as.dgC.0.factors):
1000    
1001    2006-11-01  Douglas Bates  <bates@r-project.org>
1002    
1003            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1004            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1005            <CsparseMatrix>) added
1006    
1007    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1008    
1009            * tests/matprod.R: add a variation of Harri's example
1010    
1011            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1012            recursive infinitely.
1013    
1014            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1015    
1016            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1017    
1018    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1019    
1020            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1021            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1022            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1023            satisfy the above test.
1024    
1025    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1026    
1027            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1028    
1029            * R/dgCMatrix.R: solve(a, b="missing") based on
1030            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1031            RHS = NULL.
1032    
1033            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1034            add more (needed) [t]crossprod() methods.
1035    
1036            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1037    
1038            * R/Auxiliaries.R (as_CspClass): cleanup
1039            (drop0): internal utility for "Csparse_drop(*, 0)"
1040            (.bail.out.2): encourage active feedback
1041    
1042    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1043    
1044            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1045    
1046            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1047            non-valid or 'sorted' case).
1048    
1049            * R/dsparseMatrix.R: add "chol" method.
1050            * R/ddenseMatrix.R: ditto
1051    
1052            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1053            * NAMESPACE (Ops)
1054            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1055            coercion; deprecating direct lower level coercions.
1056    
1057            * R/*.R (seq): use seq_len() and seq_along() where possible.
1058    
1059    
1060    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1061    
1062            * DESCRIPTION (Version): 0.9975-5 ready for release
1063    
1064    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1065    
1066            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1067    
1068    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1069    
1070            * R/AllClass.R (corMatrix): add 'validity' check;
1071                    comment out unused "LDL" class definition
1072            * NAMESPACE: mention, but do not export "LDL" class
1073            * R/corMatrix.R: new (simple), needed for R-devel with
1074            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1075              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1076    
1077    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1078    
1079            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1080            use Rprintf and R's error handling.
1081    
1082    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1083    
1084            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1085            * tests/matprod.R: add tests for the bug fixed.
1086    
1087    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1088    
1089            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1090            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1091    
1092    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1093    
1094            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1095    
1096    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1097    
1098            * DESCRIPTION (Version): 0.9975-3
1099    
1100            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1101            (sparse) matrices.
1102            * man/bdiag.Rd: docu + examples
1103    
1104            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1105    
1106            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1107            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1108    
1109            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1110            that result is sparse or diagonal (and not dense).
1111    
1112            * man/Subassign-methods.Rd: fix examples
1113    
1114            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1115            should always return a sparse (and not sometimes a diagonal) matrix.
1116    
1117    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1118    
1119            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1120    
1121    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1122    
1123            * DESCRIPTION (Version): 0.9975-2
1124    
1125            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1126    
1127    2006-10-02  Douglas Bates  <bates@R-project.org>
1128    
1129            * tests/dg_Matrix.R: Simplify test taking into account new code.
1130    
1131    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1132    
1133            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1134    
1135            * R/lsTMatrix.R: new files w/ missing methods
1136            * R/nsTMatrix.R:  "  'for completeness'
1137    
1138            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1139    
1140            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1141    
1142    
1143    2006-09-28  Douglas Bates  <bates@R-project.org>
1144    
1145            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1146            included.
1147    
1148            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1149            Export C-callable functions used in Zt_create in lme4.
1150    
1151    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1152    
1153            * DESCRIPTION (Version): 0.9975-1
1154    
1155            * tests/simple.R: less checks fail; using NA, found that our
1156                    kronecker() is not base-compatible with NA's.
1157    
1158            * R/dMatrix.R: "Compare" method now implemented for all cases
1159    
1160            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1161    
1162            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1163    
1164            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1165            * src/dspMatrix.c (dspMatrix_validate): ditto
1166    
1167            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1168              including coercion to [nl]tTMatrix.
1169    
1170            * R/diagMatrix.R (show): print a header line as for other classes.
1171    
1172    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1173    
1174            * src/Makefile.win (SUBDIRS): fix typo
1175    
1176    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1177    
1178            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1179    
1180    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1181    
1182            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1183            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1184            accept a symmetric matrix).
1185            * tests/group-methods.R: Uncomment test of crossprod applied to
1186            lsCMatrix objects.
1187    
1188    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1189    
1190            * R/AllClass.R (symmetricMatrix): add validity method (available
1191            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1192    
1193            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1194    
1195            * tests/indexing.Rout.save:
1196            * tests/indexing.R: additions, mainly for 'lsparse'
1197    
1198            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1199            case.
1200    
1201            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1202    
1203    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1204    
1205            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1206                    as 'N' (1-letter - Ok?)
1207    
1208            * tests/group-methods.R: add test for logical + NAs
1209    
1210            * R/dMatrix.R ("Compare"): fix to work with NA's
1211    
1212            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1213    
1214            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1215                    which is implemented.
1216    
1217    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1218    
1219            * src/chm_common.c: coerce logical <-> double instead of
1220            typecasting;  needed for "l" matrix handling in cholmod.
1221    
1222            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1223    
1224            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1225            (Tsp2grNEL): other fixes needed
1226    
1227    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1228    
1229            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1230                    Matrices, since "lMatrix", also "lsparseM" can have NA
1231            * R/ndenseMatrix.R, etc: new source files
1232            * man/nsparseMatrix-classes.Rd, etc: new help files
1233            * tests/: adaptions
1234            * src/chm_common.c (chm_dense_to_SEXP): and others:
1235                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1236            * src/Csparse.c, etc: ditto
1237    
1238    2006-09-11  Douglas Bates  <bates@R-project.org>
1239    
1240            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1241            alloc_d**Matrix functions to the lme4 package.
1242    
1243    2006-09-09  Douglas Bates  <bates@R-project.org>
1244    
1245            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1246            fixed
1247    
1248    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1249    
1250            * R/lMatrix.R: new
1251    
1252            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1253    
1254            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1255            * man/tcrossprod.Rd: ditto
1256    
1257    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1258    
1259            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1260            for exported functions
1261            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1262            Remove partitioning algorithms for sparse matrix reordering.  The
1263            copyright on the Metis code was problematic and the methods were
1264            rarely used.
1265            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1266            operations are now done entirely in CHOLMOD code.
1267    
1268    2006-09-06  Douglas Bates  <bates@R-project.org>
1269    
1270            * src/Mutils.h: Remove functions that are no longer used.
1271    
1272  2006-09-04  Douglas Bates  <bates@R-project.org>  2006-09-04  Douglas Bates  <bates@R-project.org>
1273    
1274          * src/dtCMatrix.c (dtCMatrix_validate): rename functions.          * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
# Line 24  Line 1295 
1295    
1296          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1297          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1298          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
1299          * R/Csparse.R: dito          * R/Csparse.R: ditto
1300    
1301  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1302    
# Line 41  Line 1312 
1312    
1313          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1314          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1315          (.is.diagonal): dito          (.is.diagonal): ditto
1316    
1317          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1318    

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