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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1738, Tue Jan 23 17:17:15 2007 UTC
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1    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
4    
5            * R/Ops.R ("Logic"): and other "Ops", many updates
6    
7    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * src/Mutils.h (SET_DimNames): new utility
10    
11            * R/Auxiliaries.R (nnzero): improved and now exported via
12    
13            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
14    
15    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/diagMatrix.R (!): fix typo.
18    
19    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/Auxiliaries.R (as_Csparse): and quite a few others:
22                    allow to pass class definition --> speedup
23            * R/sparseMatrix.R: apply the above
24    
25            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
26    
27            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
28            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
29            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
30    
31            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
32    
33            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
34            and use it for "sparse*" as well, since it's faster than the
35            as_Csparse(.) way.
36    
37    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
40    
41    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
44            as method for   M[ ij ] <- v
45            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
46    
47            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
48            FALSE answer
49    
50            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
51            * tests/indexing.R: test it, and some of the above
52    
53    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/Auxiliaries.R (is_duplicatedT): new utility
56    
57    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
58    
59            * src/init.c (R_init_Matrix): export cholmod_scale
60    
61    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
64            base::as.matrix to (x, ...)
65    
66    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
69            file; start using "Logic", hence
70    
71            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
72            * NAMESPACE: import and export "Logic"
73    
74    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
77            only needed previously to R version 2.5.0.
78    
79    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
82    
83            * R/Tsparse.R (replTmat): fix subassignment of triangular
84            * R/Csparse.R (replCmat): ditto
85            * tests/indexing.R: more tests, incl the above fix
86    
87    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/Auxiliaries.R (drop0): extend for non CSparse
90            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
91    
92            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
93                    use uplo correctly (!); other places: use uplo_P() macro
94    
95            * R/Csparse.R (replCmat): call diagU2N() when needed
96            * R/Tsparse.R (replTmat): ditto
97    
98            * src/dtCMatrix.c (tCMatrix_validate): new
99            * src/dtTMatrix.c (tTMatrix_validate): new, used in
100            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
101    
102            * R/diagMatrix.R (replDiag): to use in [<-
103    
104    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
107                    also more general diagU2N().
108    
109    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
112            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
113    
114    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * tests/bind.R: a few more cases
117            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
118    
119            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
120            * R/ddenseMatrix.R (cbind2/rbind2)
121            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
122            * tests/indexing.R
123            * tests/indexing.Rout.save: updated
124    
125    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
128            * tests/indexing.R
129    
130    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
133            align with proper position of "0", i.e., right for integers.
134            argument 'align' by default is "fancy".
135    
136    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
139            * R/Csparse.R: and fix "Compare" for more cases.
140            * tests/Class+Meth.R: test some of these (m == m, m != m)
141    
142    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/lsparseMatrix.R: all() and any() methods
145            * R/ldenseMatrix.R:      ditto
146            * NAMESPACE, R/Matrix.R: ditto
147    
148            * man/all-methods.Rd: document them minimally
149    
150            * tests/simple.R: add a few examples for these
151    
152    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Tsparse.R ([): fix long standing typo in symmetric case
155            * man/dsCMatrix-class.Rd: add example exhibiting the above case
156    
157    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
158    
159            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
160            to LL before converting to a sparse matrix. (The LDL form can be
161            converted to a sparse matrix but it is implicitly a unit
162            triangular matrix and a diagonal matrix overwritten on the diagonal.)
163    
164    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
165    
166            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
167    
168    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
169    
170            * DESCRIPTION (Version): updated -> release 0.9975-7
171            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
172    
173    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
176    
177    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
178    
179            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
180            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
181            is exactly singular.
182    
183    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * DESCRIPTION (Date): updated -> release 0.9975-6
186    
187    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
190            now returns symmetric.
191    
192            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
193    
194            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
195            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
196    
197            * R/Auxiliaries.R (.type.kind): added
198    
199    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
202            running src/CSparse_install.sh
203    
204            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
205    
206    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
209            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
210    
211            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
212    
213            * tests/Class+Meth.R (tstMatrixClass): now assure
214            the (important in method programming) property :
215    
216                    ###>>  Every "Matrix" is either
217                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
218    
219                    (where "*" stands for "Matrix")
220    
221            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
222    
223            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
224            * tests/validObj.R: checks for "comparison"
225    
226            * R/sparseMatrix.R ([): improved indexing for sparse;
227                    trying to keep <symmetric>[ n, n] symmmetric
228    
229            * tests/indexing.R: indexing for logical sparse now ok
230    
231    
232    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * src/Tsparse.c: use xTsparse_validate() , and hence remove
235    
236            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
237    
238    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
241    
242            * tests/simple.R: validObject() checking the above.
243    
244            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
245            replacing both dgCMatrix_validate and lgCM*.
246    
247            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
248            fix dimnames setting in other places.
249            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
250    
251    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
254    
255            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
256            symmetry test, via
257            * R/Auxiliaries.R (.as.dgC.0.factors):
258    
259    2006-11-01  Douglas Bates  <bates@r-project.org>
260    
261            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
262            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
263            <CsparseMatrix>) added
264    
265    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * tests/matprod.R: add a variation of Harri's example
268    
269            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
270            recursive infinitely.
271    
272            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
273    
274            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
275    
276    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
279            matrix if possible; test m+m == 2*m; now test dgRMatrix.
280            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
281            satisfy the above test.
282    
283    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
286    
287            * R/dgCMatrix.R: solve(a, b="missing") based on
288            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
289            RHS = NULL.
290    
291            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
292            add more (needed) [t]crossprod() methods.
293    
294            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
295    
296            * R/Auxiliaries.R (as_CspClass): cleanup
297            (drop0): internal utility for "Csparse_drop(*, 0)"
298            (.bail.out.2): encourage active feedback
299    
300    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dMatrix.R(Compare): new(), then slots [no validity check]
303    
304            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
305            non-valid or 'sorted' case).
306    
307            * R/dsparseMatrix.R: add "chol" method.
308            * R/ddenseMatrix.R: ditto
309    
310            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
311            * NAMESPACE (Ops)
312            * R/diagMatrix.R (diag2T): simple utility used "higher level"
313            coercion; deprecating direct lower level coercions.
314    
315            * R/*.R (seq): use seq_len() and seq_along() where possible.
316    
317    
318    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * DESCRIPTION (Version): 0.9975-5 ready for release
321    
322    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
323    
324            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
325    
326    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/AllClass.R (corMatrix): add 'validity' check;
329                    comment out unused "LDL" class definition
330            * NAMESPACE: mention, but do not export "LDL" class
331            * R/corMatrix.R: new (simple), needed for R-devel with
332            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
333              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
334    
335    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
336    
337            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
338            use Rprintf and R's error handling.
339    
340    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
343            * tests/matprod.R: add tests for the bug fixed.
344    
345    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
346    
347            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
348            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
349    
350    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
351    
352            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
353    
354    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * DESCRIPTION (Version): 0.9975-3
357    
358            * R/diagMatrix.R (bdiag): new function constructing block diagonal
359            (sparse) matrices.
360            * man/bdiag.Rd: docu + examples
361    
362            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
363    
364            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
365            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
366    
367            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
368            that result is sparse or diagonal (and not dense).
369    
370            * man/Subassign-methods.Rd: fix examples
371    
372            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
373            should always return a sparse (and not sometimes a diagonal) matrix.
374    
375    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
378    
379    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
380    
381            * DESCRIPTION (Version): 0.9975-2
382    
383            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
384    
385    2006-10-02  Douglas Bates  <bates@R-project.org>
386    
387            * tests/dg_Matrix.R: Simplify test taking into account new code.
388    
389    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
392    
393            * R/lsTMatrix.R: new files w/ missing methods
394            * R/nsTMatrix.R:  "  'for completeness'
395    
396            * tests/Class+Meth.R: a bit less 'not.ok.classes'
397    
398            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
399    
400    
401    2006-09-28  Douglas Bates  <bates@R-project.org>
402    
403            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
404            included.
405    
406            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
407            Export C-callable functions used in Zt_create in lme4.
408    
409    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * DESCRIPTION (Version): 0.9975-1
412    
413            * tests/simple.R: less checks fail; using NA, found that our
414                    kronecker() is not base-compatible with NA's.
415    
416            * R/dMatrix.R: "Compare" method now implemented for all cases
417    
418            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
419    
420            * man/dtpMatrix-class.Rd: mention length of 'x' slot
421    
422            * src/dtpMatrix.c (dtpMatrix_validate): fix check
423            * src/dspMatrix.c (dspMatrix_validate): ditto
424    
425            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
426              including coercion to [nl]tTMatrix.
427    
428            * R/diagMatrix.R (show): print a header line as for other classes.
429    
430    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * src/Makefile.win (SUBDIRS): fix typo
433    
434    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
437    
438    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
439    
440            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
441            symmetric and y missing in R code using %*% (cholmod_aat doesn't
442            accept a symmetric matrix).
443            * tests/group-methods.R: Uncomment test of crossprod applied to
444            lsCMatrix objects.
445    
446    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
447    
448            * R/AllClass.R (symmetricMatrix): add validity method (available
449            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
450    
451            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
452    
453            * tests/indexing.Rout.save:
454            * tests/indexing.R: additions, mainly for 'lsparse'
455    
456            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
457            case.
458    
459            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
460    
461    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
464                    as 'N' (1-letter - Ok?)
465    
466            * tests/group-methods.R: add test for logical + NAs
467    
468            * R/dMatrix.R ("Compare"): fix to work with NA's
469    
470            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
471    
472            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
473                    which is implemented.
474    
475    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * src/chm_common.c: coerce logical <-> double instead of
478            typecasting;  needed for "l" matrix handling in cholmod.
479    
480            * tests/other-pkgs.R (graph): small extension in "graph" checks.
481    
482            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
483            (Tsp2grNEL): other fixes needed
484    
485    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
488                    Matrices, since "lMatrix", also "lsparseM" can have NA
489            * R/ndenseMatrix.R, etc: new source files
490            * man/nsparseMatrix-classes.Rd, etc: new help files
491            * tests/: adaptions
492            * src/chm_common.c (chm_dense_to_SEXP): and others:
493                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
494            * src/Csparse.c, etc: ditto
495    
496    2006-09-11  Douglas Bates  <bates@R-project.org>
497    
498            * src/Mutils.[ch],init.c inst/include/*.h: Move the
499            alloc_d**Matrix functions to the lme4 package.
500    
501    2006-09-09  Douglas Bates  <bates@R-project.org>
502    
503            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
504            fixed
505    
506    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
507    
508            * R/lMatrix.R: new
509    
510            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
511    
512            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
513            * man/tcrossprod.Rd: ditto
514    
515    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
516    
517            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
518            for exported functions
519            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
520            Remove partitioning algorithms for sparse matrix reordering.  The
521            copyright on the Metis code was problematic and the methods were
522            rarely used.
523            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
524            operations are now done entirely in CHOLMOD code.
525    
526    2006-09-06  Douglas Bates  <bates@R-project.org>
527    
528            * src/Mutils.h: Remove functions that are no longer used.
529    
530    2006-09-04  Douglas Bates  <bates@R-project.org>
531    
532            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
533            * src/DEPS.mkf: update
534    
535    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * created branches/Matrix-for-R-2.3.x;  on trunk: do
538            * DESCRIPTION (Version): 0.9975-0
539            (Depends): R (>= 2.4.0)
540    
541    2006-09-01  Douglas Bates  <bates@R-project.org>
542    
543            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
544    
545    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
546    
547            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
548            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
549    
550            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
551    
552    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
555            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
556            * R/dsparseMatrix.R: ditto
557            * R/Csparse.R: ditto
558    
559    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * R/dMatrix.R (Compare): improve availability of "<", etc
562            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
563    
564    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
565    
566            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
567            of a 0-index which was used as 1-index (..hmm)
568    
569            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
570    
571            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
572            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
573            (.is.diagonal): ditto
574    
575            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
576    
577            * R/Matrix.R (Matrix): also work for NA data
578    
579    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
580    
581            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
582            in all cases.
583    
584    2006-08-27  Douglas Bates  <bates@R-project.org>
585    
586            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
587            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
588    
589    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
592            subclasses of "ddenseMatrix"
593            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
594            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
595            instead of half dozen specialized ones.
596    
597    2006-08-25  Douglas Bates  <bates@R-project.org>
598    
599            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
600            <tillard@cirad.fr> - ordering standard errors to match effects.
601    
602    2006-08-24  Douglas Bates  <bates@R-project.org>
603    
604            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
605            on R_ldl.
606            * R/lCholCMatrix.R,
607            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
608            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
609            * many files in ./R and ./src: Use more general version of
610            dup_mMatrix_as_dgeMatrix to simplify method definitions.
611            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
612            dtpMatrix, dspMatrix and dppMatrix conversions.
613    
614    
615    2006-08-23  Douglas Bates  <bates@R-project.org>
616    
617            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
618            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
619            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
620            dgeMatrix_crossprod (may need to do this in other places).
621            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
622            generic and method for dsCMatrix.  Use CHOLMOD for chol().
623    
624    2006-08-22  Douglas Bates  <bates@R-project.org>
625    
626            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
627            types of classed Matrices, matrices or numeric or logical vectors.
628            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
629            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
630            to Mutils.h (as an inline) and change name to Matrix_check_class;
631            fixes in as_cholmod_factor and chm_factor_to_SEXP.
632            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
633            dsCMatrix_matrix_solve.  Comment out vestigial functions.
634            * src/Csparse.c: use diag_P and uplo_P macros.
635    
636    2006-08-21  Douglas Bates  <bates@R-project.org>
637    
638            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
639            valgrind.
640            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
641            inverses.
642            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
643            -Wall warnings.
644            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
645            Use dup_mMatrix_as_dgeMatrix.
646    
647    2006-08-20  Douglas Bates  <bates@R-project.org>
648    
649            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
650            * tests/sparseQR.R: Added
651            * man/sparseQR-class.Rd: Document methods for qr.* generics
652            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
653    
654    2006-08-19  Douglas Bates  <bates@R-project.org>
655    
656            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
657            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
658            and qr.fitted.
659            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
660            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
661    
662    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
665            the base version has no "..." argument.
666    
667            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
668    
669            * R/Matrix.R: define and
670            * NAMESPACE: export as.numeric() and as.logical() methods.
671                    Let's hope these do not badly slow down something...
672            Finally export the zapsmall() method.
673    
674    2006-08-17  Douglas Bates  <bates@R-project.org>
675    
676            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
677            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
678            * src/dtCMatrix.c :Remove code that is no longer used
679            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
680    
681    2006-08-14  Douglas Bates  <bates@R-project.org>
682    
683            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
684            Csparse_to_logical and Csparse_symmetric_to_general.
685            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
686            coercion methods between CsparseMatrix and TsparseMatrix.
687    
688    2006-08-14  Douglas Bates  <bates@R-project.org>
689    
690            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
691            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
692            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
693            possible.
694    
695  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
696    
697          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,

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