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revision 1507, Mon Sep 4 18:41:34 2006 UTC revision 2096, Fri Dec 7 17:44:44 2007 UTC
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1    
2    
3    >>>>>> FIXME  rcond(matrix(1:6, 2,3))   gives infinite recursion !!! <<<<<<<<<<
4    
5    
6    
7    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/sparseMatrix.R (cov2cor): method for sparse matrices
10    
11            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
12    
13            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
14    
15            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
16    
17    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/Matrix.R: "generic" cov2cor() method
20    
21            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
22                    speed up Q %*% D %*% t(Q)
23            * tests/dpoMatrix.R: test nearPD()
24    
25    2007-12-05  Doug Bates and Martin Maechler
26    
27            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
28            stats::xtabs() allowing to create sparse matrices.
29    
30    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
33    
34    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
37    
38    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * R/LU.R: solve() method for "denseLU"
41    
42    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * DESCRIPTION (Version): 0.999375-3 preparing for release
45    
46            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
47    
48            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
49    
50    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
53              thanks to Kasper Kristensen.
54            * tests/matprod.R: regression test for that.
55    
56    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
57    
58            * [r4778] R/AllGeneric.R: Check R version before defining generics for
59              primitives
60    
61    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/denseMatrix.R (rcond): method
64            * R/sparseQR.R (rcond): method, use x or t(x)
65    
66    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
69            matrices.
70            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
71    
72            * man/rcond.Rd: mention the more general definition, and add
73            example for non-square matrices.
74    
75            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
76    
77    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
80    
81    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
84            * tests/indexing.R: add new regression for the above cases.
85    
86    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * src/Mutils.h (__sun): clause for alloca.h on Solaris
89    
90    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * DESCRIPTION (Date, Version): 0.999375-2
93    
94    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/HBMM.R (readMM): make work for pattern matrices as well
97    
98    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
99    
100            * [r4730] src/Mutils.h: declare alloca
101            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
102              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
103              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
104              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
105              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
106              methods; switch writeMM to use CHOLMOD code; repair readMM
107    
108    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
111            Oehlschlaegel's ... result type still to be discussed!
112    
113    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * man/image-methods.Rd: new, combining all image() methods
116    
117    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
120            to work via dgC...
121    
122            * R/Matrix.R (Matrix): special treatment for "table" (S3)
123    
124    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * R/dgTMatrix.R (image): change defaults to
127                    aspect = "iso", colorkey = FALSE
128    
129    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
132            must copy its *expanded* x slot before LAPACK call.
133    
134            * tests/matprod.R: test the last days' changes.
135    
136    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
137    
138            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
139              as well as in sources
140            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
141              Lapack call
142    
143    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
146                    ("Matrix", "matrix") which is needed in some cases.
147            Ditto for solve().
148    
149            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
150            infinite recursion in dispatch for some cases.
151    
152    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
153    
154            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
155              so pointers match
156    
157    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * DESCRIPTION (Date): set ready for release -- 0.999375-1
160    
161    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
162    
163            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
164              src/chm_common.c, src/chm_common.h: Change API for
165              numeric_as_chm_dense and N_AS_CHM_DN
166    
167    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
170            * tests/matprod.R: regr.test for it
171    
172    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
175            * tests/group-methods.R: and regression-test it
176    
177    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
178    
179            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
180              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
181              triplet_to_sparse, documentation, use typedefs
182    
183    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * man/dpoMatrix-class.Rd: added 'corMatrix' example
186    
187            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
188            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
189            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
190    
191            * R/lsparseMatrix.R: bug fix in "all" method
192            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
193    
194            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
195            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
196                    + matrix |-> nMatrix coercion
197            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
198            * man/pMatrix-class.Rd: ditto
199    
200            * R/Matrix.R (Summary): method for non-dMatrix
201    
202            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
203            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
204                    test all Summary methods.
205    
206    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
209    
210    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
213    
214            * R/pMatrix.R (t?crossprod): methods for pMatrix
215    
216    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
217    
218            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
219    
220    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
221    
222            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
223              trying to fix a subtle bug - which has been somewhere else.
224    
225    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
226    
227            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
228              solve the bug
229    
230    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * src/dgCMatrix.c (compressed_to_TMatrix):
233    
234    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * src/Csparse.c (Rsparse_validate): new, to have some validity
237            checking for RsparseMatrix
238            * src/dgCMatrix.c (xRMatrix_validate): ditto
239            * src/dtCMatrix.c (tRMatrix_validate): ditto
240    
241    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
242    
243            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
244              lgRMatrix
245            * [r4568] DESCRIPTION: Prepare for bug-fix release
246            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
247              for declaration of cholmod_symmetry
248    
249    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
252            release.
253    
254    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
255    
256            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
257              functions - no longer used
258            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
259              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
260              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
261              Alloca
262    
263    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
264    
265            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
266              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
267              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
268              src/t_gCMatrix_colSums.c: more R_CheckStack()s
269    
270    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
271    
272            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
273              the required amount of memory then call M_numeric_as_chm_dense.
274            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
275              (like Calloc but calling alloca)
276    
277    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
280            and extended with more sophisticated 'col.names' option.
281            * NAMESPACE: export  printSparseMatrix()
282            * man/printSpMatrix.Rd: document, incl. examples
283    
284    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
285    
286            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
287              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
288              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
289    
290    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * DESCRIPTION (Version): 0.99875-4
293    
294            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
295            some dimnames perservation.
296    
297            * R/dsTMatrix.R (t-method): keep dimnames
298            * R/dtTMatrix.R:  ditto
299    
300            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
301            and ncol(.) < 10
302    
303            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
304            from Mutils.h
305    
306            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
307            e.g. in as(<ngCMatrix>, "matrix")
308    
309    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
310    
311            * [r4529] .: Create a branch for the API changes from the 0.99875
312              series to the 0.999375 series
313            * [r4530] DESCRIPTION, inst/include/Matrix.h,
314              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
315              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
316              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
317              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
318              as_cholmod_x functions
319    
320    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
321    
322            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
323              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
324              to Comparisons
325    
326    >>>>>>> .merge-right.r4561
327    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * DESCRIPTION (Version): 0.99875-3 ready to be released.
330    
331            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
332    
333            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
334            that should also work in a future version of R.
335    
336    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
339    
340            * R/sparseVector.R: more *sparseVector coercions, notably for
341            non - double ones.
342    
343    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
346              notably the new ones building on the new .Call(.)s:
347    
348            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
349            all 4 of [dlin]gCMatrix_colSums().
350    
351    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
352    
353            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
354            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
355              result
356    
357    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/kronecker.R: fix typo (could lead to inf.recursion)
360            * test/simple.R: testing that
361    
362            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
363            method as well (which can have arguments, show() can't).
364    
365    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
366    
367            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
368              added dgCMatrix_colSums for [col,row][Sums,Means]
369    
370    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
371    
372            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
373              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
374              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
375            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
376              class
377            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
378              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
379              row names to store the levels - duh!  Added an example.
380    
381    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * src/Csparse.c (Csparse_validate): check for *repeated* entries
384            thanks to example from Christian Buchta; with a test here:
385            * tests/simple.R:
386    
387    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
390            of colSums(*, sparseResult = TRUE)
391    
392    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
395            'na.rm = FALSE' as "everywhere" else in R.
396    
397    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
398    
399            * [r4421] src/CSparse_install.sh: Modify for new organization of
400              CSparse package
401            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
402              SuiteSparse
403            * [r4426] src/Makefile: add ./UFconfig to the include path for
404              compilation
405            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
406            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
407              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
408    
409    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
412            * R/sparseMatrix.R (prSpMatrix): now gives a message about
413            suppressed column names.
414    
415    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
416    
417            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
418              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
419              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
420              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
421              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
422              Remove warnings after change to const char* CHAR
423    
424    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
425    
426            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
427              type of M_cholmod_ssmult
428    
429    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
430    
431            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
432              src/init.c: Yet another cholmod export - cholmod_ssmult
433    
434    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * NAMESPACE: exported drop0(), since
437            * man/drop0.Rd: I have seen several cases, I really wanted to use
438            it, so our users may want too.
439    
440    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * man/colSums.Rd: separately document colSums() etc, since these
443            have the extra argument 'sparseResult'.
444    
445    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
448            * man/spMatrix.Rd: docu., including examples
449    
450            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
451            in order to make colMeans() etc fast *and* correct.
452            * R/sparseVector.R (replSPvec): "[<-" functionality for
453            sparseVectors; tested in
454            * tests/simple.R:
455    
456    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
459            (very) sparse Matrices; output similar to Matlab's print().
460    
461    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
462    
463            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
464            0-based, indices (Jose Quesada <quesada@gmail.com>).
465    
466    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
467    
468            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
469    
470    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * R/Auxiliaries.R (sparsapply): new utility, much faster than
473            tapply1() for large sparse matrices.
474    
475    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * R/Matrix.R (dim<-): reshape now via sparseVector.
478    
479            * R/sparseVector.R: methods and function for
480            * R/AllClass.R: new "sparseVector" class and daughters.
481            * NAMESPACE: export new classes
482    
483    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
484    
485            * DESCRIPTION (Version): 0.99875-1
486            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
487    
488    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
489    
490            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
491            indexing
492            * tests/indexing.R: test set for that.
493    
494    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
497            entries.
498            * tests/indexing.R(out): add regression test for it
499    
500    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
503            name for "!" method definitions.
504    
505    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * R/Tsparse.R (intI): new utility, used for "[" :
508                    Cleanup up there, and fixes for duplicated indices - more TODO!
509    
510            * tests/indexing.R(out): more tests
511    
512    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
513    
514            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
515            code that is now part of the R Lapack library.
516    
517            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
518            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
519    
520    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
523    
524    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
527            up with extraneous names '0'...'<n-1>'
528    
529    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * R/dgTMatrix.R (mat2dgT): care about NAs
532    
533    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/kronecker.R: triangularity preserving methods
536    
537    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * R/kronecker.R: new file collecting kronecker() methods in one
540                    place.  Goal: become much faster!
541    
542    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
545            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
546            can be much faster.
547    
548            * tests/matprod.R: add regression tests for these (upper & lower).
549    
550    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
551    
552            * R/Matrix.R (diff): method for our Matrices.
553    
554            * R/sparseMatrix.R (isDiagonal): check dim()!
555    
556    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * R/Matrix.R (dim<-): new method for "reshape()" built on a
559            proposal from Tamas Papp.
560    
561    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
564    
565            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
566            rather define and export  cBind() and rBind() only.
567            --> useRs *must* change code that used to have cbind()/rbind() !!
568    
569            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
570            * R/bind.Rout.save: ditto
571    
572    2007-02-16  Douglas Bates  <bates@r-project.org>
573    
574            * DESCRIPTION (Date, Version): 0.9975-11 with new date
575            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
576            const modifier on declaration of the array 'valid'
577    
578    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
579    
580            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
581    
582    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
585    
586            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
587            * tests/simple.R: test the above and some of these coercions:
588    
589            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
590                    be careful to avoid infinite recursion, using new coercions in
591            * R/ngCMatrix.R and nsC... and ntC...
592            * R/lsparseMatrix.R: ditto
593    
594            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
595    
596            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
597            * R/Rsparse.R: reactivate .Call()s
598    
599            * tests/Class+Meth.R: a bit more on actual classes
600    
601    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
602    
603            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
604    
605    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * DESCRIPTION (Version): 0.9975-10 to upload
608    
609            * tests/Class+Meth.R (tstMatrixClass): require coercions to
610            specific classes less unconditionally.
611    
612            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
613    
614            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
615    
616            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
617            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
618            R_to_CMatrix segfaults on one platform.
619            Eliminate most coercion method to *specific* classes, and replace
620            with virtual classes coercions.
621    
622    
623    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
624    
625            * src/init.c: export the CHM...._validate() placeholders, since
626            they *are* called.
627    
628            * tests/Class+Meth.R (classCanCoerce): and starting to test
629            all as(<from>, <to>)
630    
631    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
632    
633            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
634            * tests/indexing.R: tested now
635            * tests/indexing.Rout.save: updated
636    
637            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
638            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
639            appropriate.
640    
641            * NAMESPACE: export a trivial
642            * R/Matrix.R: drop() Matrix-method
643    
644            * R/AllClass.R: moved all prototypes to virtual super classes.
645    
646            * R/Rsparse.R: many more coercions to have less exceptions in
647            * tests/Class+Meth.R:
648    
649            * R/Ops.R (Compare): tweak for case with NA
650            * tests/simpl.R: hence another 'FIXME' eliminated
651    
652    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
653    
654            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
655            objects.
656    
657            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
658              and more of "!", "&", "|", all, any; coercions
659    
660            * R/Rsparse.R: many coercions (which enable quite a few other
661            methods), thanks to enhancements in
662            * src/dgCMatrix.c (R_to_CMatrix): new, and
663            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
664            symmetric & triangular and ..RMatrix objects.
665    
666            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
667            renamed file from src/dsTMatrix.c;
668            now dealing with symmetric and triangular Tsparse coercions, both
669            to dense and general.
670    
671    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
674    
675            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
676            where sensible when the <numeric> is of length > 1.
677    
678    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * R/Matrix.R ([<-): for M[] <- value: fix length
681    
682    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
685            * R/ndenseMatrix.R: new coercions n* -> l*
686    
687    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
690    
691            * R/Ops.R ("Logic"): and other "Ops", many updates
692    
693    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * src/Mutils.h (SET_DimNames): new utility
696    
697            * R/Auxiliaries.R (nnzero): improved and now exported via
698    
699            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
700    
701    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * R/diagMatrix.R (!): fix typo.
704    
705    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
706    
707            * R/Auxiliaries.R (as_Csparse): and quite a few others:
708                    allow to pass class definition --> speedup
709            * R/sparseMatrix.R: apply the above
710    
711            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
712    
713            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
714            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
715            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
716    
717            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
718    
719            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
720            and use it for "sparse*" as well, since it's faster than the
721            as_Csparse(.) way.
722    
723    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
724    
725            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
726    
727    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
730            as method for   M[ ij ] <- v
731            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
732    
733            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
734            FALSE answer
735    
736            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
737            * tests/indexing.R: test it, and some of the above
738    
739    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * R/Auxiliaries.R (is_duplicatedT): new utility
742    
743    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
744    
745            * src/init.c (R_init_Matrix): export cholmod_scale
746    
747    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
750            base::as.matrix to (x, ...)
751    
752    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
755            file; start using "Logic", hence
756    
757            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
758            * NAMESPACE: import and export "Logic"
759    
760    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
761    
762            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
763            only needed previously to R version 2.5.0.
764    
765    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
768    
769            * R/Tsparse.R (replTmat): fix subassignment of triangular
770            * R/Csparse.R (replCmat): ditto
771            * tests/indexing.R: more tests, incl the above fix
772    
773    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * R/Auxiliaries.R (drop0): extend for non CSparse
776            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
777    
778            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
779                    use uplo correctly (!); other places: use uplo_P() macro
780    
781            * R/Csparse.R (replCmat): call diagU2N() when needed
782            * R/Tsparse.R (replTmat): ditto
783    
784            * src/dtCMatrix.c (tCMatrix_validate): new
785            * src/dtTMatrix.c (tTMatrix_validate): new, used in
786            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
787    
788            * R/diagMatrix.R (replDiag): to use in [<-
789    
790    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
793                    also more general diagU2N().
794    
795    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
798            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
799    
800    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
801    
802            * tests/bind.R: a few more cases
803            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
804    
805            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
806            * R/ddenseMatrix.R (cbind2/rbind2)
807            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
808            * tests/indexing.R
809            * tests/indexing.Rout.save: updated
810    
811    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
812    
813            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
814            * tests/indexing.R
815    
816    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
817    
818            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
819            align with proper position of "0", i.e., right for integers.
820            argument 'align' by default is "fancy".
821    
822    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
823    
824            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
825            * R/Csparse.R: and fix "Compare" for more cases.
826            * tests/Class+Meth.R: test some of these (m == m, m != m)
827    
828    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
829    
830            * R/lsparseMatrix.R: all() and any() methods
831            * R/ldenseMatrix.R:      ditto
832            * NAMESPACE, R/Matrix.R: ditto
833    
834            * man/all-methods.Rd: document them minimally
835    
836            * tests/simple.R: add a few examples for these
837    
838    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
839    
840            * R/Tsparse.R ([): fix long standing typo in symmetric case
841            * man/dsCMatrix-class.Rd: add example exhibiting the above case
842    
843    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
844    
845            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
846            to LL before converting to a sparse matrix. (The LDL form can be
847            converted to a sparse matrix but it is implicitly a unit
848            triangular matrix and a diagonal matrix overwritten on the diagonal.)
849    
850    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
851    
852            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
853    
854    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
855    
856            * DESCRIPTION (Version): updated -> release 0.9975-7
857            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
858    
859    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
860    
861            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
862    
863    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
864    
865            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
866            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
867            is exactly singular.
868    
869    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
870    
871            * DESCRIPTION (Date): updated -> release 0.9975-6
872    
873    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
874    
875            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
876            now returns symmetric.
877    
878            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
879    
880            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
881            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
882    
883            * R/Auxiliaries.R (.type.kind): added
884    
885    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
886    
887            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
888            running src/CSparse_install.sh
889    
890            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
891    
892    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
893    
894            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
895            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
896    
897            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
898    
899            * tests/Class+Meth.R (tstMatrixClass): now assure
900            the (important in method programming) property :
901    
902                    ###>>  Every "Matrix" is either
903                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
904    
905                    (where "*" stands for "Matrix")
906    
907            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
908    
909            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
910            * tests/validObj.R: checks for "comparison"
911    
912            * R/sparseMatrix.R ([): improved indexing for sparse;
913                    trying to keep <symmetric>[ n, n] symmmetric
914    
915            * tests/indexing.R: indexing for logical sparse now ok
916    
917    
918    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
919    
920            * src/Tsparse.c: use xTsparse_validate() , and hence remove
921    
922            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
923    
924    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
925    
926            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
927    
928            * tests/simple.R: validObject() checking the above.
929    
930            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
931            replacing both dgCMatrix_validate and lgCM*.
932    
933            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
934            fix dimnames setting in other places.
935            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
936    
937    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
938    
939            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
940    
941            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
942            symmetry test, via
943            * R/Auxiliaries.R (.as.dgC.0.factors):
944    
945    2006-11-01  Douglas Bates  <bates@r-project.org>
946    
947            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
948            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
949            <CsparseMatrix>) added
950    
951    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
952    
953            * tests/matprod.R: add a variation of Harri's example
954    
955            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
956            recursive infinitely.
957    
958            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
959    
960            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
961    
962    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
963    
964            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
965            matrix if possible; test m+m == 2*m; now test dgRMatrix.
966            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
967            satisfy the above test.
968    
969    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
970    
971            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
972    
973            * R/dgCMatrix.R: solve(a, b="missing") based on
974            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
975            RHS = NULL.
976    
977            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
978            add more (needed) [t]crossprod() methods.
979    
980            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
981    
982            * R/Auxiliaries.R (as_CspClass): cleanup
983            (drop0): internal utility for "Csparse_drop(*, 0)"
984            (.bail.out.2): encourage active feedback
985    
986    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
987    
988            * R/dMatrix.R(Compare): new(), then slots [no validity check]
989    
990            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
991            non-valid or 'sorted' case).
992    
993            * R/dsparseMatrix.R: add "chol" method.
994            * R/ddenseMatrix.R: ditto
995    
996            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
997            * NAMESPACE (Ops)
998            * R/diagMatrix.R (diag2T): simple utility used "higher level"
999            coercion; deprecating direct lower level coercions.
1000    
1001            * R/*.R (seq): use seq_len() and seq_along() where possible.
1002    
1003    
1004    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1005    
1006            * DESCRIPTION (Version): 0.9975-5 ready for release
1007    
1008    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1009    
1010            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1011    
1012    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1013    
1014            * R/AllClass.R (corMatrix): add 'validity' check;
1015                    comment out unused "LDL" class definition
1016            * NAMESPACE: mention, but do not export "LDL" class
1017            * R/corMatrix.R: new (simple), needed for R-devel with
1018            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1019              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1020    
1021    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1022    
1023            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1024            use Rprintf and R's error handling.
1025    
1026    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1027    
1028            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1029            * tests/matprod.R: add tests for the bug fixed.
1030    
1031    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1032    
1033            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1034            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1035    
1036    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1037    
1038            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1039    
1040    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1041    
1042            * DESCRIPTION (Version): 0.9975-3
1043    
1044            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1045            (sparse) matrices.
1046            * man/bdiag.Rd: docu + examples
1047    
1048            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1049    
1050            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1051            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1052    
1053            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1054            that result is sparse or diagonal (and not dense).
1055    
1056            * man/Subassign-methods.Rd: fix examples
1057    
1058            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1059            should always return a sparse (and not sometimes a diagonal) matrix.
1060    
1061    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1062    
1063            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1064    
1065    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1066    
1067            * DESCRIPTION (Version): 0.9975-2
1068    
1069            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1070    
1071    2006-10-02  Douglas Bates  <bates@R-project.org>
1072    
1073            * tests/dg_Matrix.R: Simplify test taking into account new code.
1074    
1075    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1076    
1077            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1078    
1079            * R/lsTMatrix.R: new files w/ missing methods
1080            * R/nsTMatrix.R:  "  'for completeness'
1081    
1082            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1083    
1084            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1085    
1086    
1087    2006-09-28  Douglas Bates  <bates@R-project.org>
1088    
1089            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1090            included.
1091    
1092            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1093            Export C-callable functions used in Zt_create in lme4.
1094    
1095    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1096    
1097            * DESCRIPTION (Version): 0.9975-1
1098    
1099            * tests/simple.R: less checks fail; using NA, found that our
1100                    kronecker() is not base-compatible with NA's.
1101    
1102            * R/dMatrix.R: "Compare" method now implemented for all cases
1103    
1104            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1105    
1106            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1107    
1108            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1109            * src/dspMatrix.c (dspMatrix_validate): ditto
1110    
1111            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1112              including coercion to [nl]tTMatrix.
1113    
1114            * R/diagMatrix.R (show): print a header line as for other classes.
1115    
1116    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1117    
1118            * src/Makefile.win (SUBDIRS): fix typo
1119    
1120    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1121    
1122            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1123    
1124    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1125    
1126            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1127            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1128            accept a symmetric matrix).
1129            * tests/group-methods.R: Uncomment test of crossprod applied to
1130            lsCMatrix objects.
1131    
1132    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1133    
1134            * R/AllClass.R (symmetricMatrix): add validity method (available
1135            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1136    
1137            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1138    
1139            * tests/indexing.Rout.save:
1140            * tests/indexing.R: additions, mainly for 'lsparse'
1141    
1142            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1143            case.
1144    
1145            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1146    
1147    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1148    
1149            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1150                    as 'N' (1-letter - Ok?)
1151    
1152            * tests/group-methods.R: add test for logical + NAs
1153    
1154            * R/dMatrix.R ("Compare"): fix to work with NA's
1155    
1156            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1157    
1158            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1159                    which is implemented.
1160    
1161    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1162    
1163            * src/chm_common.c: coerce logical <-> double instead of
1164            typecasting;  needed for "l" matrix handling in cholmod.
1165    
1166            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1167    
1168            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1169            (Tsp2grNEL): other fixes needed
1170    
1171    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1172    
1173            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1174                    Matrices, since "lMatrix", also "lsparseM" can have NA
1175            * R/ndenseMatrix.R, etc: new source files
1176            * man/nsparseMatrix-classes.Rd, etc: new help files
1177            * tests/: adaptions
1178            * src/chm_common.c (chm_dense_to_SEXP): and others:
1179                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1180            * src/Csparse.c, etc: ditto
1181    
1182    2006-09-11  Douglas Bates  <bates@R-project.org>
1183    
1184            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1185            alloc_d**Matrix functions to the lme4 package.
1186    
1187    2006-09-09  Douglas Bates  <bates@R-project.org>
1188    
1189            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1190            fixed
1191    
1192    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1193    
1194            * R/lMatrix.R: new
1195    
1196            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1197    
1198            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1199            * man/tcrossprod.Rd: ditto
1200    
1201    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1202    
1203            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1204            for exported functions
1205            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1206            Remove partitioning algorithms for sparse matrix reordering.  The
1207            copyright on the Metis code was problematic and the methods were
1208            rarely used.
1209            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1210            operations are now done entirely in CHOLMOD code.
1211    
1212    2006-09-06  Douglas Bates  <bates@R-project.org>
1213    
1214            * src/Mutils.h: Remove functions that are no longer used.
1215    
1216  2006-09-04  Douglas Bates  <bates@R-project.org>  2006-09-04  Douglas Bates  <bates@R-project.org>
1217    
1218          * src/dtCMatrix.c (dtCMatrix_validate): rename functions.          * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
# Line 24  Line 1239 
1239    
1240          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1241          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1242          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
1243          * R/Csparse.R: dito          * R/Csparse.R: ditto
1244    
1245  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1246    
# Line 41  Line 1256 
1256    
1257          * 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
1258          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1259          (.is.diagonal): dito          (.is.diagonal): ditto
1260    
1261          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1262    

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